34211a
usecases/Miseq-16S/16S-ref-db-PE-splice.pl	cd-hit
usecases/Miseq-16S/NG-Omics-Miseq-16S.pl	cd-hit
usecases/Miseq-16S/NG-Omics-WF.pl	cd-hit
usecases/Miseq-16S/README	cd-hit
usecases/Miseq-16S/cd-hit-otu-miseq-PE.pl	cd-hit
usecases/Miseq-16S/clstr_2_OTU_table.pl	cd-hit
usecases/Miseq-16S/filter-chimeric-and-small.pl	cd-hit
usecases/Miseq-16S/filter-chimeric-by-ref.pl	cd-hit
usecases/Miseq-16S/filter-nontop-ref.pl	cd-hit
usecases/Miseq-16S/filter-refonly-cluster.pl	cd-hit
usecases/Miseq-16S/greengene-ann1.pl	cd-hit
usecases/Miseq-16S/pool_samples.pl	cd-hit
vars.config.in	erlang-p1-iconv,erlang-p1-pam,erlang-p1-sip,erlang-p1-stringprep,erlang-p1-tls,erlang-p1-xml,erlang-p1-yaml,erlang-p1-zlib
.
34210a
unitig.c	fermi-lite
.
34196a
tools/uni_parse.tcl	erlang-p1-stringprep
tools/uni_parse2.tcl	erlang-p1-stringprep
.
34027a
tests/rfc4475/badaspec.dat	erlang-p1-sip
tests/rfc4475/badbranch.dat	erlang-p1-sip
tests/rfc4475/baddate.dat	erlang-p1-sip
tests/rfc4475/baddn.dat	erlang-p1-sip
tests/rfc4475/badinv01.dat	erlang-p1-sip
tests/rfc4475/badvers.dat	erlang-p1-sip
tests/rfc4475/bcast.dat	erlang-p1-sip
tests/rfc4475/bext01.dat	erlang-p1-sip
tests/rfc4475/bigcode.dat	erlang-p1-sip
tests/rfc4475/clerr.dat	erlang-p1-sip
tests/rfc4475/cparam01.dat	erlang-p1-sip
tests/rfc4475/cparam02.dat	erlang-p1-sip
tests/rfc4475/dblreq.dat	erlang-p1-sip
tests/rfc4475/esc01.dat	erlang-p1-sip
tests/rfc4475/esc02.dat	erlang-p1-sip
tests/rfc4475/escnull.dat	erlang-p1-sip
tests/rfc4475/escruri.dat	erlang-p1-sip
tests/rfc4475/insuf.dat	erlang-p1-sip
tests/rfc4475/intmeth.dat	erlang-p1-sip
tests/rfc4475/inv2543.dat	erlang-p1-sip
tests/rfc4475/invut.dat	erlang-p1-sip
tests/rfc4475/longreq.dat	erlang-p1-sip
tests/rfc4475/ltgtruri.dat	erlang-p1-sip
tests/rfc4475/lwsdisp.dat	erlang-p1-sip
tests/rfc4475/lwsruri.dat	erlang-p1-sip
tests/rfc4475/lwsstart.dat	erlang-p1-sip
tests/rfc4475/mcl01.dat	erlang-p1-sip
tests/rfc4475/mismatch01.dat	erlang-p1-sip
tests/rfc4475/mismatch02.dat	erlang-p1-sip
tests/rfc4475/mpart01.dat	erlang-p1-sip
tests/rfc4475/multi01.dat	erlang-p1-sip
tests/rfc4475/ncl.dat	erlang-p1-sip
tests/rfc4475/noreason.dat	erlang-p1-sip
tests/rfc4475/novelsc.dat	erlang-p1-sip
tests/rfc4475/quotbal.dat	erlang-p1-sip
tests/rfc4475/regaut01.dat	erlang-p1-sip
tests/rfc4475/regbadct.dat	erlang-p1-sip
tests/rfc4475/regescrt.dat	erlang-p1-sip
tests/rfc4475/scalar02.dat	erlang-p1-sip
tests/rfc4475/scalarlg.dat	erlang-p1-sip
tests/rfc4475/sdp01.dat	erlang-p1-sip
tests/rfc4475/semiuri.dat	erlang-p1-sip
tests/rfc4475/test.dat	erlang-p1-sip
tests/rfc4475/transports.dat	erlang-p1-sip
tests/rfc4475/trws.dat	erlang-p1-sip
tests/rfc4475/unkscm.dat	erlang-p1-sip
tests/rfc4475/unksm2.dat	erlang-p1-sip
tests/rfc4475/unreason.dat	erlang-p1-sip
tests/rfc4475/wsinv.dat	erlang-p1-sip
tests/rfc4475/zeromf.dat	erlang-p1-sip
tests/rfc5118/ipv4-mapped-ipv6	erlang-p1-sip
tests/rfc5118/ipv6-bad	erlang-p1-sip
tests/rfc5118/ipv6-bug-abnf-3-colons	erlang-p1-sip
tests/rfc5118/ipv6-correct-abnf-2-colons	erlang-p1-sip
tests/rfc5118/ipv6-good	erlang-p1-sip
tests/rfc5118/ipv6-in-sdp	erlang-p1-sip
tests/rfc5118/mult-ip-in-header	erlang-p1-sip
tests/rfc5118/mult-ip-in-sdp	erlang-p1-sip
tests/rfc5118/port-ambiguous	erlang-p1-sip
tests/rfc5118/port-unambiguous	erlang-p1-sip
tests/rfc5118/via-received-param-no-delim	erlang-p1-sip
tests/rfc5118/via-received-param-with-delim	erlang-p1-sip
.
34021a
tests/cert.pem	erlang-p1-tls
.
34005a
test/zlib_test.erl	erlang-p1-zlib
.
33889a
test/tests.erl	erlang-p1-stringprep
.
33862a
test/test_helper.exs	erlang-p1-xml
.
33852a
test/test1.yml	erlang-p1-yaml
test/test2.yml	erlang-p1-yaml
test/test3.yml	erlang-p1-yaml
test/test4.yml	erlang-p1-yaml
.
33845a
test/meck_args_matcher_tests.erl	erlang-meck
test/meck_expect_tests.erl	erlang-meck
test/meck_history_tests.erl	erlang-meck
test/meck_matcher_tests.erl	erlang-meck
test/meck_on_load_module.erl	erlang-meck
test/meck_on_load_tests.erl	erlang-meck
test/meck_performance_test.erl	erlang-meck
test/meck_ret_spec_tests.erl	erlang-meck
test/meck_test_module.erl	erlang-meck
test/meck_tests.erl	erlang-meck
test/oauth2_mock_backend.erl	erlang-p1-oauth2
test/oauth2_priv_set_tests.erl	erlang-p1-oauth2
test/oauth2_response_tests.erl	erlang-p1-oauth2
test/oauth2_tests.erl	erlang-p1-oauth2
test/oauth2_token_tests.erl	erlang-p1-oauth2
test/p1_queue_test.erl	erlang-p1-utils
.
33843a
test/jiffy_01_yajl_tests.erl	erlang-jiffy
test/jiffy_02_literal_tests.erl	erlang-jiffy
test/jiffy_03_number_tests.erl	erlang-jiffy
test/jiffy_04_string_tests.erl	erlang-jiffy
test/jiffy_05_array_tests.erl	erlang-jiffy
test/jiffy_06_object_tests.erl	erlang-jiffy
test/jiffy_07_compound_tests.erl	erlang-jiffy
test/jiffy_08_halfword_tests.erl	erlang-jiffy
test/jiffy_09_reg_issue_24_tests.erl	erlang-jiffy
test/jiffy_10_short_double_tests.erl	erlang-jiffy
test/jiffy_11_property_tests.erl	erlang-jiffy
test/jiffy_12_error_tests.erl	erlang-jiffy
test/jiffy_13_whitespace_tests.erl	erlang-jiffy
test/jiffy_15_return_trailer_tests.erl	erlang-jiffy
test/jiffy_util.hrl	erlang-jiffy
.
33841a
test/include/cover_test.hrl	erlang-meck
.
33839a
test/fxml_test.erl	erlang-p1-xml
.
33838a
test/elixir/fast_xml_test.exs	erlang-p1-xml
test/elixir/fxml_test.exs	erlang-p1-xml
.
33693a
test/cover_test_module.dontcompile	erlang-meck
.
33670a
test/cache_tab_test.erl	erlang-p1-cache-tab
test/cases/array.eterm	erlang-jiffy
test/cases/array.json	erlang-jiffy
test/cases/array_close.eterm	erlang-jiffy
test/cases/array_close.json	erlang-jiffy
test/cases/array_open.eterm	erlang-jiffy
test/cases/array_open.json	erlang-jiffy
test/cases/bogus_char.eterm	erlang-jiffy
test/cases/bogus_char.json	erlang-jiffy
test/cases/codepoints_from_unicode_org.eterm	erlang-jiffy
test/cases/codepoints_from_unicode_org.json	erlang-jiffy
test/cases/deep_arrays.eterm	erlang-jiffy
test/cases/deep_arrays.json	erlang-jiffy
test/cases/difficult_json_c_test_case.eterm	erlang-jiffy
test/cases/difficult_json_c_test_case.json	erlang-jiffy
test/cases/doubles.eterm	erlang-jiffy
test/cases/doubles.json	erlang-jiffy
test/cases/empty_array.eterm	erlang-jiffy
test/cases/empty_array.json	erlang-jiffy
test/cases/empty_string.eterm	erlang-jiffy
test/cases/empty_string.json	erlang-jiffy
test/cases/escaped_bulgarian.eterm	erlang-jiffy
test/cases/escaped_bulgarian.json	erlang-jiffy
test/cases/escaped_foobar.eterm	erlang-jiffy
test/cases/escaped_foobar.json	erlang-jiffy
test/cases/false.eterm	erlang-jiffy
test/cases/false.json	erlang-jiffy
test/cases/false_then_garbage.eterm	erlang-jiffy
test/cases/false_then_garbage.json	erlang-jiffy
test/cases/four_byte_utf8.eterm	erlang-jiffy
test/cases/four_byte_utf8.json	erlang-jiffy
test/cases/integers.eterm	erlang-jiffy
test/cases/integers.json	erlang-jiffy
test/cases/invalid_utf8.eterm	erlang-jiffy
test/cases/invalid_utf8.json	erlang-jiffy
test/cases/isolated_surrogate_marker.eterm	erlang-jiffy
test/cases/isolated_surrogate_marker.json	erlang-jiffy
test/cases/leading_zero_in_number.eterm	erlang-jiffy
test/cases/leading_zero_in_number.json	erlang-jiffy
test/cases/lonely_minus_sign.eterm	erlang-jiffy
test/cases/lonely_minus_sign.json	erlang-jiffy
test/cases/lonely_number.eterm	erlang-jiffy
test/cases/lonely_number.json	erlang-jiffy
test/cases/map_close.eterm	erlang-jiffy
test/cases/map_close.json	erlang-jiffy
test/cases/map_open.eterm	erlang-jiffy
test/cases/map_open.json	erlang-jiffy
test/cases/missing_integer_after_decimal_point.eterm	erlang-jiffy
test/cases/missing_integer_after_decimal_point.json	erlang-jiffy
test/cases/missing_integer_after_exponent.eterm	erlang-jiffy
test/cases/missing_integer_after_exponent.json	erlang-jiffy
test/cases/non_utf8_char_in_string.eterm	erlang-jiffy
test/cases/non_utf8_char_in_string.json	erlang-jiffy
test/cases/null.eterm	erlang-jiffy
test/cases/null.json	erlang-jiffy
test/cases/null_then_garbage.eterm	erlang-jiffy
test/cases/null_then_garbage.json	erlang-jiffy
test/cases/nulls_and_bools.eterm	erlang-jiffy
test/cases/nulls_and_bools.json	erlang-jiffy
test/cases/short-doubles.txt	erlang-jiffy
test/cases/simple.eterm	erlang-jiffy
test/cases/simple.json	erlang-jiffy
test/cases/string_invalid_escape.eterm	erlang-jiffy
test/cases/string_invalid_escape.json	erlang-jiffy
test/cases/string_invalid_hex_char.eterm	erlang-jiffy
test/cases/string_invalid_hex_char.json	erlang-jiffy
test/cases/string_with_escapes.eterm	erlang-jiffy
test/cases/string_with_escapes.json	erlang-jiffy
test/cases/string_with_invalid_newline.eterm	erlang-jiffy
test/cases/string_with_invalid_newline.json	erlang-jiffy
test/cases/three_byte_utf8.eterm	erlang-jiffy
test/cases/three_byte_utf8.json	erlang-jiffy
test/cases/true.eterm	erlang-jiffy
test/cases/true.json	erlang-jiffy
test/cases/true_then_garbage.eterm	erlang-jiffy
test/cases/true_then_garbage.json	erlang-jiffy
test/cases/unescaped_bulgarian.eterm	erlang-jiffy
test/cases/unescaped_bulgarian.json	erlang-jiffy
.
33640a
test/MT-simu.fq.gz	fermi-lite
.
33319a
support/query_dsdt.pl	acpi-call
support/windump_hack/windump.c	acpi-call
support/windump_hack/xorg.conf	acpi-call
.
33302a
src/xdata_codec.erl	erlang-p1-xmpp
src/xep0004.erl	erlang-p1-xmpp
src/xep0012.erl	erlang-p1-xmpp
src/xep0013.erl	erlang-p1-xmpp
src/xep0016.erl	erlang-p1-xmpp
src/xep0022.erl	erlang-p1-xmpp
src/xep0023.erl	erlang-p1-xmpp
src/xep0030.erl	erlang-p1-xmpp
src/xep0033.erl	erlang-p1-xmpp
src/xep0039.erl	erlang-p1-xmpp
src/xep0045.erl	erlang-p1-xmpp
src/xep0048.erl	erlang-p1-xmpp
src/xep0049.erl	erlang-p1-xmpp
src/xep0050.erl	erlang-p1-xmpp
src/xep0054.erl	erlang-p1-xmpp
src/xep0055.erl	erlang-p1-xmpp
src/xep0059.erl	erlang-p1-xmpp
src/xep0060.erl	erlang-p1-xmpp
src/xep0065.erl	erlang-p1-xmpp
src/xep0066.erl	erlang-p1-xmpp
src/xep0077.erl	erlang-p1-xmpp
src/xep0078.erl	erlang-p1-xmpp
src/xep0085.erl	erlang-p1-xmpp
src/xep0092.erl	erlang-p1-xmpp
src/xep0114.erl	erlang-p1-xmpp
src/xep0115.erl	erlang-p1-xmpp
src/xep0131.erl	erlang-p1-xmpp
src/xep0138.erl	erlang-p1-xmpp
src/xep0153.erl	erlang-p1-xmpp
src/xep0158.erl	erlang-p1-xmpp
src/xep0172.erl	erlang-p1-xmpp
src/xep0191.erl	erlang-p1-xmpp
src/xep0198.erl	erlang-p1-xmpp
src/xep0199.erl	erlang-p1-xmpp
src/xep0202.erl	erlang-p1-xmpp
src/xep0203.erl	erlang-p1-xmpp
src/xep0220.erl	erlang-p1-xmpp
src/xep0221.erl	erlang-p1-xmpp
src/xep0231.erl	erlang-p1-xmpp
src/xep0249.erl	erlang-p1-xmpp
src/xep0264.erl	erlang-p1-xmpp
src/xep0279.erl	erlang-p1-xmpp
src/xep0280.erl	erlang-p1-xmpp
src/xep0297.erl	erlang-p1-xmpp
src/xep0313.erl	erlang-p1-xmpp
src/xep0334.erl	erlang-p1-xmpp
src/xep0352.erl	erlang-p1-xmpp
src/xep0355.erl	erlang-p1-xmpp
src/xep0356.erl	erlang-p1-xmpp
src/xep0357.erl	erlang-p1-xmpp
src/xep0359.erl	erlang-p1-xmpp
src/xep0363.erl	erlang-p1-xmpp
src/xep0369.erl	erlang-p1-xmpp
src/xmpp.app.src	erlang-p1-xmpp
src/xmpp.erl	erlang-p1-xmpp
src/xmpp_codec.erl	erlang-p1-xmpp
src/xmpp_codec_external.erl	erlang-p1-xmpp
src/xmpp_tr.erl	erlang-p1-xmpp
src/xmpp_util.erl	erlang-p1-xmpp
.
33199a
src/turn.erl	erlang-p1-stun
src/turn_sm.erl	erlang-p1-stun
src/turn_tmp_sup.erl	erlang-p1-stun
.
33197a
src/treap.erl	erlang-p1-utils
.
33190a
src/stringprep.app.src	erlang-p1-stringprep
src/stringprep.erl	erlang-p1-stringprep
src/stringprep_app.erl	erlang-p1-stringprep
src/stringprep_sup.erl	erlang-p1-stringprep
src/stun.app.src	erlang-p1-stun
src/stun.erl	erlang-p1-stun
src/stun_app.erl	erlang-p1-stun
src/stun_codec.erl	erlang-p1-stun
src/stun_listener.erl	erlang-p1-stun
src/stun_shaper.erl	erlang-p1-stun
src/stun_sup.erl	erlang-p1-stun
src/stun_test.erl	erlang-p1-stun
src/stun_tmp_sup.erl	erlang-p1-stun
.
33126a
src/rfc3921.erl	erlang-p1-xmpp
src/rfc6120.erl	erlang-p1-xmpp
src/rfc6121.erl	erlang-p1-xmpp
.
33114a
src/pubsub_get_pending.erl	erlang-p1-xmpp
src/pubsub_node_config.erl	erlang-p1-xmpp
src/pubsub_publish_options.erl	erlang-p1-xmpp
src/pubsub_subscribe_authorization.erl	erlang-p1-xmpp
src/pubsub_subscribe_options.erl	erlang-p1-xmpp
.
32752a
src/pgsql.erl	erlang-p1-pgsql
src/pgsql_app.erl	erlang-p1-pgsql
src/pgsql_proto.erl	erlang-p1-pgsql
src/pgsql_socket.erl	erlang-p1-pgsql
src/pgsql_sup.erl	erlang-p1-pgsql
src/pgsql_util.erl	erlang-p1-pgsql
.
32742a
src/p1_edoc_layout.erl	erlang-p1-utils
src/p1_file_queue.erl	erlang-p1-utils
src/p1_fsm.erl	erlang-p1-utils
src/p1_http.erl	erlang-p1-utils
src/p1_mucsub.erl	erlang-p1-xmpp
src/p1_mysql.app.src	erlang-p1-mysql
src/p1_mysql.erl	erlang-p1-mysql
src/p1_mysql_app.erl	erlang-p1-mysql
src/p1_mysql_auth.erl	erlang-p1-mysql
src/p1_mysql_conn.erl	erlang-p1-mysql
src/p1_mysql_recv.erl	erlang-p1-mysql
src/p1_mysql_sup.erl	erlang-p1-mysql
src/p1_nif_utils.erl	erlang-p1-utils
src/p1_oauth2.app.src	erlang-p1-oauth2
src/p1_options.erl	erlang-p1-utils
src/p1_pgsql.app.src	erlang-p1-pgsql
src/p1_queue.erl	erlang-p1-utils
src/p1_server.erl	erlang-p1-utils
src/p1_sha.erl	erlang-p1-tls
src/p1_time_compat.erl	erlang-p1-utils
src/p1_utils.app.src	erlang-p1-utils
src/p1_utils.erl	erlang-p1-utils
src/p1_utils_sup.erl	erlang-p1-utils
.
32735a
src/oauth2.erl	erlang-p1-oauth2
src/oauth2_backend.erl	erlang-p1-oauth2
src/oauth2_config.erl	erlang-p1-oauth2
src/oauth2_priv_set.erl	erlang-p1-oauth2
src/oauth2_response.erl	erlang-p1-oauth2
src/oauth2_token.erl	erlang-p1-oauth2
src/oauth2_token_generation.erl	erlang-p1-oauth2
.
32728a
src/muc_register.erl	erlang-p1-xmpp
src/muc_request.erl	erlang-p1-xmpp
src/muc_roomconfig.erl	erlang-p1-xmpp
src/muc_roominfo.erl	erlang-p1-xmpp
.
32724a
src/mash/Command.cpp	mash
src/mash/Command.h	mash
src/mash/CommandBounds.cpp	mash
src/mash/CommandBounds.h	mash
src/mash/CommandContain.cpp	mash
src/mash/CommandContain.h	mash
src/mash/CommandDistance.cpp	mash
src/mash/CommandDistance.h	mash
src/mash/CommandFind.cpp	mash
src/mash/CommandFind.h	mash
src/mash/CommandInfo.cpp	mash
src/mash/CommandInfo.h	mash
src/mash/CommandList.cpp	mash
src/mash/CommandList.h	mash
src/mash/CommandPaste.cpp	mash
src/mash/CommandPaste.h	mash
src/mash/CommandSketch.cpp	mash
src/mash/CommandSketch.h	mash
src/mash/HashList.cpp	mash
src/mash/HashList.h	mash
src/mash/HashPriorityQueue.cpp	mash
src/mash/HashPriorityQueue.h	mash
src/mash/HashSet.cpp	mash
src/mash/HashSet.h	mash
src/mash/MinHashHeap.cpp	mash
src/mash/MinHashHeap.h	mash
src/mash/MurmurHash3.cpp	mash
src/mash/MurmurHash3.h	mash
src/mash/Sketch.cpp	mash
src/mash/Sketch.h	mash
src/mash/ThreadPool.h	mash
src/mash/ThreadPool.hxx	mash
src/mash/bloom_filter.hpp	mash
src/mash/capnp/MinHash.capnp	mash
src/mash/hash.cpp	mash
src/mash/hash.h	mash
src/mash/kseq.h	mash
src/mash/mash.cpp	mash
src/mash/memcpyLink.h	mash
src/mash/memcpyWrap.c	mash
src/mash/sketchParameterSetup.cpp	mash
src/mash/sketchParameterSetup.h	mash
src/mash/version.h	mash
src/meck.app.src	erlang-meck
src/meck.erl	erlang-meck
src/meck_args_matcher.erl	erlang-meck
src/meck_code.erl	erlang-meck
src/meck_code_gen.erl	erlang-meck
src/meck_cover.erl	erlang-meck
src/meck_expect.erl	erlang-meck
src/meck_history.erl	erlang-meck
src/meck_matcher.erl	erlang-meck
src/meck_proc.erl	erlang-meck
src/meck_ret_spec.erl	erlang-meck
src/meck_util.erl	erlang-meck
.
32721a
src/mam_query.erl	erlang-p1-xmpp
.
32467a
src/jid.erl	erlang-p1-xmpp
src/jiffy.app.src	erlang-jiffy
src/jiffy.erl	erlang-jiffy
src/jiffy_utf8.erl	erlang-jiffy
.
32462a
src/iconv.app.src	erlang-p1-iconv
src/iconv.erl	erlang-p1-iconv
src/iconv_app.erl	erlang-p1-iconv
src/iconv_sup.erl	erlang-p1-iconv
.
32440a
src/fxml.erl	erlang-p1-xml
src/fxml_gen.erl	erlang-p1-xml
src/fxml_gen_pt.erl	erlang-p1-xml
src/fxml_stream.erl	erlang-p1-xml
src/fxml_sup.erl	erlang-p1-xml
src/fxmlrpc.erl	erlang-p1-xml
src/fxmlrpc_codec.erl	erlang-p1-xml
.
32435a
src/flex_offline.erl	erlang-p1-xmpp
.
32431a
src/ezlib.app.src	erlang-p1-zlib
src/ezlib.erl	erlang-p1-zlib
src/ezlib_app.erl	erlang-p1-zlib
src/ezlib_sup.erl	erlang-p1-zlib
src/fast_tls.app.src	erlang-p1-tls
src/fast_tls.erl	erlang-p1-tls
src/fast_tls_app.erl	erlang-p1-tls
src/fast_tls_sup.erl	erlang-p1-tls
src/fast_xml.app.src	erlang-p1-xml
src/fast_xml.erl	erlang-p1-xml
src/fast_yaml.app.src	erlang-p1-yaml
src/fast_yaml.erl	erlang-p1-yaml
src/fast_yaml_app.erl	erlang-p1-yaml
src/fast_yaml_sup.erl	erlang-p1-yaml
.
32422a
src/epam.app.src	erlang-p1-pam
src/epam.erl	erlang-p1-pam
src/epam_app.erl	erlang-p1-pam
src/epam_sup.erl	erlang-p1-pam
src/esip.app.src	erlang-p1-sip
src/esip.erl	erlang-p1-sip
src/esip_app.erl	erlang-p1-sip
src/esip_client_transaction.erl	erlang-p1-sip
src/esip_codec.erl	erlang-p1-sip
src/esip_dialog.erl	erlang-p1-sip
src/esip_listener.erl	erlang-p1-sip
src/esip_server_transaction.erl	erlang-p1-sip
src/esip_socket.erl	erlang-p1-sip
src/esip_sup.erl	erlang-p1-sip
src/esip_tmp_sup.erl	erlang-p1-sip
src/esip_transaction.erl	erlang-p1-sip
src/esip_transport.erl	erlang-p1-sip
src/esip_udp_sup.erl	erlang-p1-sip
src/ets_cache.erl	erlang-p1-cache-tab
src/ets_cache_options.erl	erlang-p1-cache-tab
.
31909a
src/cache_tab.app.src	erlang-p1-cache-tab
src/cache_tab.erl	erlang-p1-cache-tab
src/cache_tab_app.erl	erlang-p1-cache-tab
src/cache_tab_sup.erl	erlang-p1-cache-tab
.
31206a
spec/README.md	erlang-p1-xml
spec/fxmlrpc_codec.spec	erlang-p1-xml
specs/flex_offline.cfg	erlang-p1-xmpp
specs/flex_offline.xdata	erlang-p1-xmpp
specs/mam_query.cfg	erlang-p1-xmpp
specs/mam_query.xdata	erlang-p1-xmpp
specs/muc_register.cfg	erlang-p1-xmpp
specs/muc_register.xdata	erlang-p1-xmpp
specs/muc_request.cfg	erlang-p1-xmpp
specs/muc_request.xdata	erlang-p1-xmpp
specs/muc_roomconfig.cfg	erlang-p1-xmpp
specs/muc_roomconfig.xdata	erlang-p1-xmpp
specs/muc_roominfo.cfg	erlang-p1-xmpp
specs/muc_roominfo.xdata	erlang-p1-xmpp
specs/pubsub_get_pending.cfg	erlang-p1-xmpp
specs/pubsub_get_pending.xdata	erlang-p1-xmpp
specs/pubsub_node_config.cfg	erlang-p1-xmpp
specs/pubsub_node_config.xdata	erlang-p1-xmpp
specs/pubsub_publish_options.cfg	erlang-p1-xmpp
specs/pubsub_publish_options.xdata	erlang-p1-xmpp
specs/pubsub_subscribe_authorization.cfg	erlang-p1-xmpp
specs/pubsub_subscribe_authorization.xdata	erlang-p1-xmpp
specs/pubsub_subscribe_options.cfg	erlang-p1-xmpp
specs/pubsub_subscribe_options.xdata	erlang-p1-xmpp
specs/xmpp_codec.spec	erlang-p1-xmpp
.
31201a
sketch.c	minimap
.
31172c
setup.py	ariba,gramps,lava-dispatcher,lava-server,python-pymummer
.
31162a
sdust.c	minimap
sdust.h	minimap
.
31151a
scripts/ariba	ariba
.
30876a
rope.c	fermi-lite
rope.h	fermi-lite
.
30874a
rld0.c	fermi-lite
rld0.h	fermi-lite
rle.c	fermi-lite
rle.h	fermi-lite
.
30871a
pymummer/__init__.py	python-pymummer
pymummer/alignment.py	python-pymummer
pymummer/coords_file.py	python-pymummer
pymummer/nucmer.py	python-pymummer
pymummer/snp.py	python-pymummer
pymummer/snp_file.py	python-pymummer
pymummer/syscall.py	python-pymummer
pymummer/tests/alignment_test.py	python-pymummer
pymummer/tests/coords_file_test.py	python-pymummer
pymummer/tests/data/coords_file_test_convert_to_msp_crunch.coords	python-pymummer
pymummer/tests/data/coords_file_test_convert_to_msp_crunch.no_offset.crunch	python-pymummer
pymummer/tests/data/coords_file_test_convert_to_msp_crunch.qry.fa	python-pymummer
pymummer/tests/data/coords_file_test_convert_to_msp_crunch.qry.fa.fai	python-pymummer
pymummer/tests/data/coords_file_test_convert_to_msp_crunch.ref.fa	python-pymummer
pymummer/tests/data/coords_file_test_convert_to_msp_crunch.ref.fa.fai	python-pymummer
pymummer/tests/data/coords_file_test_convert_to_msp_crunch.with_offset.crunch	python-pymummer
pymummer/tests/data/coords_file_test_no_header.coords	python-pymummer
pymummer/tests/data/coords_file_test_with_header.coords	python-pymummer
pymummer/tests/data/nucmer_test_out.coords	python-pymummer
pymummer/tests/data/nucmer_test_out.coords.snps	python-pymummer
pymummer/tests/data/nucmer_test_qry.fa	python-pymummer
pymummer/tests/data/nucmer_test_ref.fa	python-pymummer
pymummer/tests/data/nucmer_test_write_script_no_snps.sh	python-pymummer
pymummer/tests/data/nucmer_test_write_script_with_snps.sh	python-pymummer
pymummer/tests/data/snp_file_test_get_all_variants.snps	python-pymummer
pymummer/tests/data/snp_file_test_no_header.snps	python-pymummer
pymummer/tests/data/snp_file_test_with_header.snps	python-pymummer
pymummer/tests/nucmer_test.py	python-pymummer
pymummer/tests/snp_file_test.py	python-pymummer
pymummer/tests/snp_test.py	python-pymummer
pymummer/tests/syscall_test.py	python-pymummer
pymummer/tests/variant_test.py	python-pymummer
pymummer/variant.py	python-pymummer
rebar.config	erlang-jiffy,erlang-meck,erlang-p1-cache-tab,erlang-p1-iconv,erlang-p1-mysql,erlang-p1-oauth2,erlang-p1-pam,erlang-p1-pgsql,erlang-p1-sip,erlang-p1-stringprep,erlang-p1-stun,erlang-p1-tls,erlang-p1-utils,erlang-p1-xml,erlang-p1-xmpp,erlang-p1-yaml,erlang-p1-zlib
rebar.config.script	erlang-jiffy,erlang-p1-cache-tab,erlang-p1-iconv,erlang-p1-mysql,erlang-p1-pam,erlang-p1-pgsql,erlang-p1-sip,erlang-p1-stringprep,erlang-p1-stun,erlang-p1-tls,erlang-p1-utils,erlang-p1-xml,erlang-p1-xmpp,erlang-p1-yaml,erlang-p1-zlib
rebar.lock	erlang-meck
rebar.test.config	erlang-p1-oauth2
rebar.test.config.script	erlang-p1-oauth2
.
30852a
psi-cd-hit/README.psi-cd-hit	cd-hit
psi-cd-hit/cd-hit-div.pl	cd-hit
psi-cd-hit/clstr_select_rep.pl	cd-hit
psi-cd-hit/clstr_select_seq.pl	cd-hit
psi-cd-hit/fetch_fasta_by_ids.pl	cd-hit
psi-cd-hit/fetch_fasta_exclude_ids.pl	cd-hit
psi-cd-hit/psi-2d.pl	cd-hit
psi-cd-hit/psi-cd-hit-local-old.pl	cd-hit
psi-cd-hit/psi-cd-hit-local.pl	cd-hit
psi-cd-hit/psi-cd-hit-old.pl	cd-hit
psi-cd-hit/psi-cd-hit.pl	cd-hit
psi-cd-hit/qsub-template	cd-hit
.
30776a
plugins/rebar_gdb_plugin.erl	erlang-jiffy
.
30767a
plot_2d.pl	cd-hit
plot_len1.pl	cd-hit
.
27614a
mrope.c	fermi-lite
mrope.h	fermi-lite
.
27574a
missing	erlang-p1-iconv
mix.exs	erlang-p1-xml
.
27544a
minimap.1	minimap
minimap.h	minimap
misc.c	fermi-lite,minimap
.
27541a
map.c	minimap
.
27512a
mag.c	fermi-lite
mag.h	fermi-lite
main.c	minimap
make_multi_seq.pl	cd-hit
.
26810c
license.txt	calendar-exchange-provider,cd-hit
.
26723a
lib/fast_xml.ex	erlang-p1-xml
.
25542a
kdq.h	minimap
khash.h	fermi-lite,minimap
kmer.h	fermi-lite
kseq.h	fermi-lite,minimap
ksort.h	fermi-lite,minimap
kstring.h	fermi-lite
ksw.c	fermi-lite
ksw.h	fermi-lite
kthread.c	fermi-lite,minimap
kvec.h	fermi-lite,minimap
.
25533a
internal.h	fermi-lite
.
25374c
install_dependencies.sh	ariba,python-pymummer,roary
.
25372a
include/xmpp.hrl	erlang-p1-xmpp
include/xmpp_codec.hrl	erlang-p1-xmpp
index.c	minimap
install-sh	erlang-p1-iconv
.
25201a
include/stun.hrl	erlang-p1-stun
.
25191a
include/pubsub_get_pending.hrl	erlang-p1-xmpp
include/pubsub_node_config.hrl	erlang-p1-xmpp
include/pubsub_publish_options.hrl	erlang-p1-xmpp
include/pubsub_subscribe_authorization.hrl	erlang-p1-xmpp
include/pubsub_subscribe_options.hrl	erlang-p1-xmpp
.
25133a
include/mam_query.hrl	erlang-p1-xmpp
include/muc_register.hrl	erlang-p1-xmpp
include/muc_request.hrl	erlang-p1-xmpp
include/muc_roomconfig.hrl	erlang-p1-xmpp
include/muc_roominfo.hrl	erlang-p1-xmpp
include/ns.hrl	erlang-p1-xmpp
include/p1_mysql.hrl	erlang-p1-mysql
include/p1_queue.hrl	erlang-p1-utils
.
25120a
include/jid.hrl	erlang-p1-xmpp
.
25116a
include/fxml.hrl	erlang-p1-xml
include/fxml_gen.hrl	erlang-p1-xml
.
25113a
include/esip.hrl	erlang-p1-sip
include/esip_lib.hrl	erlang-p1-sip
include/ets_cache.hrl	erlang-p1-cache-tab
include/flex_offline.hrl	erlang-p1-xmpp
.
24188a
htab.c	fermi-lite
htab.h	fermi-lite
.
22959a
fml.h	fermi-lite
.
22525a
examples/turn_off_gpu.sh	acpi-call
.
22508a
examples/m11xr2.sh	acpi-call
.
22492a
examples/dellL702X.sh	acpi-call
.
22476a
examples/asus1215n.sh	acpi-call
.
22456a
example.c	fermi-lite,minimap
.
22428a
enc	erlang-jiffy
.
19696a
doc/treap.html	erlang-p1-utils
.
19691a
doc/style.css	erlang-p1-utils
.
19676a
doc/sphinx/conf.py	mash
doc/sphinx/data.rst	mash
doc/sphinx/distances.rst	mash
doc/sphinx/index.rst	mash
doc/sphinx/logo_med.png	mash
doc/sphinx/sketches.rst	mash
doc/sphinx/tutorials.rst	mash
.
19647a
doc/overview-summary.html	erlang-p1-utils
doc/overview.edoc	erlang-meck,erlang-p1-utils
doc/p1_fsm.html	erlang-p1-utils
doc/p1_nif_utils.html	erlang-p1-utils
doc/p1_server.html	erlang-p1-utils
doc/p1_time_compat.html	erlang-p1-utils
.
19636a
doc/modules-frame.html	erlang-p1-utils
.
19598a
doc/logo_ejabberd.png	erlang-p1-utils
doc/logo_p1.png	erlang-p1-utils
.
19547a
doc/index.html	erlang-p1-utils
.
19453a
doc/erlang.png	erlang-p1-utils
.
19450a
doc/dokuwiki2latex.dao	cd-hit
.
19403a
doc/cd-hit-otu-miseq-Figure-1.png	cd-hit
doc/cdhit-user-guide.pdf	cd-hit
doc/cdhit-user-guide.tex	cd-hit
doc/cdhit-user-guide.wiki	cd-hit
.
19368a
doc/Figure1.png	cd-hit
doc/Figure2.png	cd-hit
doc/Figure3.png	cd-hit
doc/Figure4.png	cd-hit
.
19366a
doc/API.md	erlang-p1-xmpp
.
18473a
dialyzer.ignore-warnings	erlang-meck
.
18465c
debian/watch	acpi-call,ariba,boinc,calendar-exchange-provider,cd-hit,cockpit,erlang-jiffy,erlang-meck,erlang-p1-cache-tab,erlang-p1-iconv,erlang-p1-mysql,erlang-p1-oauth2,erlang-p1-pam,erlang-p1-pgsql,erlang-p1-sip,erlang-p1-stringprep,erlang-p1-stun,erlang-p1-tls,erlang-p1-utils,erlang-p1-xml,erlang-p1-xmpp,erlang-p1-yaml,erlang-p1-zlib,fermi-lite,gajim,golang-github-klauspost-reedsolomon,golang-github-xtaci-kcp,golang-github-xtaci-smux,gramps,haproxy,igtf-policy-bundle,kcptun,lava-dispatcher,lava-server,libbloom,libsodium,mash,minimap,open-vm-tools,python-pymummer,roary,shadowsocks-libev,simple-obfs,spades,spl-linux,tlp,webkit2gtk
.
18461c
debian/upstream/edam	cd-hit,minimap
debian/upstream/metadata	cd-hit,gramps,mash,minimap,roary,spades
.
18447a
debian/tests/target.fasta	minimap
debian/tests/test-example	ariba
.
18445a
debian/tests/query.fasta	minimap
debian/tests/run-example	mash
debian/tests/run-unit-test	cd-hit
.
18444a
debian/tests/genomes.tar.xz	mash
.
18442c
debian/tests/control	ariba,cd-hit,cockpit,fermi-lite,gramps,haproxy,lava-dispatcher,lava-server,mash,minimap,roary,spades,spl-linux
.
18439a
debian/tests/build-lib	fermi-lite,minimap
.
18438a
debian/tests.cd-hit/example.fa	cd-hit
.
18419,18421c
debian/source.lintian-overrides	erlang-jiffy,golang-github-xtaci-kcp,golang-github-xtaci-smux,kcptun,lava-server,roary,shadowsocks-libev,spades,tlp
debian/source/format	acpi-call,ariba,boinc,calendar-exchange-provider,cd-hit,cockpit,erlang-jiffy,erlang-meck,erlang-p1-cache-tab,erlang-p1-iconv,erlang-p1-mysql,erlang-p1-oauth2,erlang-p1-pam,erlang-p1-pgsql,erlang-p1-sip,erlang-p1-stringprep,erlang-p1-stun,erlang-p1-tls,erlang-p1-utils,erlang-p1-xml,erlang-p1-xmpp,erlang-p1-yaml,erlang-p1-zlib,fermi-lite,gajim,gajim-antispam,golang-github-klauspost-reedsolomon,golang-github-xtaci-kcp,golang-github-xtaci-smux,gramps,haproxy,igtf-policy-bundle,kcptun,lava-dispatcher,lava-server,libbloom,libsodium,mash,minimap,open-vm-tools,python-pymummer,roary,shadowsocks-libev,simple-obfs,spades,spl-linux,tlp,webkit2gtk
debian/source/include-binaries	boinc,haproxy,mash
.
18395c
debian/rules	acpi-call,ariba,boinc,calendar-exchange-provider,cd-hit,cockpit,erlang-jiffy,erlang-meck,erlang-p1-cache-tab,erlang-p1-iconv,erlang-p1-mysql,erlang-p1-oauth2,erlang-p1-pam,erlang-p1-pgsql,erlang-p1-sip,erlang-p1-stringprep,erlang-p1-stun,erlang-p1-tls,erlang-p1-utils,erlang-p1-xml,erlang-p1-xmpp,erlang-p1-yaml,erlang-p1-zlib,fermi-lite,gajim,gajim-antispam,golang-github-klauspost-reedsolomon,golang-github-xtaci-kcp,golang-github-xtaci-smux,gramps,haproxy,igtf-policy-bundle,kcptun,lava-dispatcher,lava-server,libbloom,libsodium,mash,minimap,open-vm-tools,python-pymummer,roary,shadowsocks-libev,simple-obfs,spades,spl-linux,tlp,webkit2gtk
.
18370a
debian/patches/use_bwa_compatible_fermi-lite.patch	ariba
debian/patches/use_debian_mathjax.patch	mash
debian/patches/use_debian_packaged_libs_for_extension.patch	ariba
.
18361c
debian/patches/series	acpi-call,ariba,boinc,cd-hit,erlang-jiffy,erlang-p1-cache-tab,erlang-p1-iconv,erlang-p1-oauth2,erlang-p1-pam,erlang-p1-sip,erlang-p1-stringprep,erlang-p1-stun,erlang-p1-tls,erlang-p1-xml,erlang-p1-xmpp,erlang-p1-yaml,fermi-lite,gajim,golang-github-xtaci-smux,gramps,haproxy,libbloom,mash,minimap,open-vm-tools,roary,shadowsocks-libev,simple-obfs,spades,webkit2gtk
.
18357a
debian/patches/rename_bseq1_t.patch	fermi-lite
debian/patches/rename_test_input.patch	ariba
.
18356a
debian/patches/rebar.test.config.patch	erlang-p1-oauth2
debian/patches/relax-pysam-version.patch	ariba
debian/patches/remove-deps.diff	erlang-p1-cache-tab,erlang-p1-iconv,erlang-p1-sip,erlang-p1-stringprep,erlang-p1-stun,erlang-p1-tls,erlang-p1-xml,erlang-p1-xmpp,erlang-p1-yaml
debian/patches/remove_git_clean	erlang-jiffy
debian/patches/rename-cdhit.patch	ariba
.
18352a
debian/patches/parallel.patch	mash
.
18350a
debian/patches/make_shared_lib	fermi-lite,minimap
debian/patches/mips-atomic.diff	erlang-p1-cache-tab
.
18349a
debian/patches/link_dynamically_against_capnp.patch	mash
.
18348a
debian/patches/hardening	fermi-lite,minimap
debian/patches/hardening.patch	mash
.
18339a
debian/patches/fix_makefile	erlang-jiffy
.
18337a
debian/patches/fix-includes.diff	erlang-p1-sip,erlang-p1-xmpp
debian/patches/fix-spades-call.patch	ariba
.
18329a
debian/patches/drop_memcpy_wrapper.patch	mash
debian/patches/enable_help2man.patch	cd-hit
debian/patches/ensure_64bit_value	minimap
debian/patches/epam_bin_path.diff	erlang-p1-pam
debian/patches/f9de643f167cfa274862d323694c1bf5b57d3be2.patch	erlang-p1-tls
.
18328a
debian/patches/disable_spades_tests.patch	ariba
.
18313a
debian/patches/bcf_seqlib.patch	fermi-lite
.
18302a
debian/patches/b87766daf8df5e84463223df538fe3c82bc89def.patch	erlang-p1-tls
.
18297a
debian/patches/a4e6a8f6a66836f62471f7fb6df3cc590689fdfa.patch	erlang-p1-sip
.
18278a
debian/patches/0002-Fix-build-4.12-copy-from-user.patch	acpi-call
.
18276a
debian/patches/0001-Fix-compatibility-with-Linux-3.17.patch	acpi-call
.
18259a
debian/mash-doc.doc-base	mash
debian/mash-doc.docs	mash
debian/mash.install	mash
debian/mash.manpages	mash
.
18251c
debian/manpages	fermi-lite,kcptun,minimap,spades
.
18245a
debian/man_src/mash-dist.1.adoc	mash
debian/man_src/mash-info.1.adoc	mash
debian/man_src/mash-paste.1.adoc	mash
debian/man_src/mash-sketch.1.adoc	mash
debian/man_src/mash.1.adoc	mash
.
18244a
debian/make_man	ariba
.
18234c
debian/links	cd-hit,spades
.
18219a
debian/libmash-dev.install	mash
.
18180,18181c
debian/install	fermi-lite,gajim-antispam,minimap,simple-obfs,spades
debian/install.in	acpi-call,igtf-policy-bundle
.
18143c
debian/gbp.conf	acpi-call,boinc,cockpit,erlang-jiffy,golang-github-klauspost-reedsolomon,gramps,haproxy,lava-dispatcher,lava-server,open-vm-tools,spades,spl-linux,tlp,webkit2gtk
.
18134a
debian/erlang-p1-pam.lintian-overrides	erlang-p1-pam
debian/erlang-p1-yaml.docs	erlang-p1-yaml
debian/examples	acpi-call
debian/extra-man-info.txt	ariba
.
18133c
debian/docs	acpi-call,cd-hit,erlang-p1-utils,erlang-p1-xml,erlang-p1-xmpp,erlang-p1-yaml,gajim-antispam,golang-github-klauspost-reedsolomon,golang-github-xtaci-kcp,golang-github-xtaci-smux,lava-dispatcher,python-pymummer,simple-obfs,spades
.
18129,18130c
debian/dkms	acpi-call,spl-linux
debian/doc-base	cd-hit,shadowsocks-libev,simple-obfs
.
18127a
debian/dh-rebar.conf	erlang-jiffy,erlang-meck,erlang-p1-cache-tab,erlang-p1-iconv,erlang-p1-mysql,erlang-p1-oauth2,erlang-p1-pam,erlang-p1-pgsql,erlang-p1-sip,erlang-p1-stringprep,erlang-p1-stun,erlang-p1-tls,erlang-p1-utils,erlang-p1-xml,erlang-p1-xmpp,erlang-p1-yaml,erlang-p1-zlib
debian/dirs	cd-hit
.
18097c
debian/copyright	acpi-call,ariba,boinc,calendar-exchange-provider,cd-hit,cockpit,erlang-jiffy,erlang-meck,erlang-p1-cache-tab,erlang-p1-iconv,erlang-p1-mysql,erlang-p1-oauth2,erlang-p1-pam,erlang-p1-pgsql,erlang-p1-sip,erlang-p1-stringprep,erlang-p1-stun,erlang-p1-tls,erlang-p1-utils,erlang-p1-xml,erlang-p1-xmpp,erlang-p1-yaml,erlang-p1-zlib,fermi-lite,gajim,gajim-antispam,golang-github-klauspost-reedsolomon,golang-github-xtaci-kcp,golang-github-xtaci-smux,gramps,haproxy,igtf-policy-bundle,kcptun,lava-dispatcher,lava-server,libbloom,libsodium,mash,minimap,open-vm-tools,python-pymummer,roary,shadowsocks-libev,simple-obfs,spades,spl-linux,tlp,webkit2gtk
.
18094c
debian/control	acpi-call,ariba,boinc,calendar-exchange-provider,cd-hit,cockpit,erlang-jiffy,erlang-meck,erlang-p1-cache-tab,erlang-p1-iconv,erlang-p1-mysql,erlang-p1-oauth2,erlang-p1-pam,erlang-p1-pgsql,erlang-p1-sip,erlang-p1-stringprep,erlang-p1-stun,erlang-p1-tls,erlang-p1-utils,erlang-p1-xml,erlang-p1-xmpp,erlang-p1-yaml,erlang-p1-zlib,fermi-lite,gajim,gajim-antispam,golang-github-klauspost-reedsolomon,golang-github-xtaci-kcp,golang-github-xtaci-smux,gramps,haproxy,igtf-policy-bundle,kcptun,lava-dispatcher,lava-server,libbloom,libsodium,mash,minimap,open-vm-tools,python-pymummer,roary,shadowsocks-libev,simple-obfs,spades,spl-linux,tlp,webkit2gtk
.
18087c
debian/compat	acpi-call,ariba,boinc,calendar-exchange-provider,cd-hit,cockpit,erlang-jiffy,erlang-meck,erlang-p1-cache-tab,erlang-p1-iconv,erlang-p1-mysql,erlang-p1-oauth2,erlang-p1-pam,erlang-p1-pgsql,erlang-p1-sip,erlang-p1-stringprep,erlang-p1-stun,erlang-p1-tls,erlang-p1-utils,erlang-p1-xml,erlang-p1-xmpp,erlang-p1-yaml,erlang-p1-zlib,fermi-lite,gajim,gajim-antispam,golang-github-klauspost-reedsolomon,golang-github-xtaci-kcp,golang-github-xtaci-smux,gramps,haproxy,igtf-policy-bundle,kcptun,lava-dispatcher,lava-server,libbloom,libsodium,mash,minimap,open-vm-tools,python-pymummer,roary,shadowsocks-libev,simple-obfs,spades,spl-linux,tlp,webkit2gtk
.
18069c
debian/cd-hit.examples	cd-hit
debian/changelog	acpi-call,ariba,boinc,calendar-exchange-provider,cd-hit,cockpit,erlang-jiffy,erlang-meck,erlang-p1-cache-tab,erlang-p1-iconv,erlang-p1-mysql,erlang-p1-oauth2,erlang-p1-pam,erlang-p1-pgsql,erlang-p1-sip,erlang-p1-stringprep,erlang-p1-stun,erlang-p1-tls,erlang-p1-utils,erlang-p1-xml,erlang-p1-xmpp,erlang-p1-yaml,erlang-p1-zlib,fermi-lite,gajim,gajim-antispam,golang-github-klauspost-reedsolomon,golang-github-xtaci-kcp,golang-github-xtaci-smux,gramps,haproxy,igtf-policy-bundle,kcptun,lava-dispatcher,lava-server,libbloom,libsodium,mash,minimap,open-vm-tools,python-pymummer,roary,shadowsocks-libev,simple-obfs,spades,spl-linux,tlp,webkit2gtk
.
18028a
debian/ariba.1.adoc	ariba
debian/ariba.manpages	ariba
.
18026c
debian/TODO	cockpit,fermi-lite
.
18024c
debian/README.package	ariba
debian/README.source	boinc,erlang-jiffy,gramps,igtf-policy-bundle
.
18022c
debian/README.Debian	boinc,cd-hit,erlang-p1-pam,gramps,haproxy,igtf-policy-bundle,lava-dispatcher,lava-server,shadowsocks-libev,tlp
.
17952a
data/refseq.msh	mash
.
17295a
data/genome1.fna	mash
data/genome2.fna	mash
data/genome3.fna	mash
.
16764,16765c
configure	cockpit,erlang-p1-iconv,erlang-p1-pam,erlang-p1-sip,erlang-p1-stringprep,erlang-p1-tls,erlang-p1-xml,erlang-p1-yaml,erlang-p1-zlib,gajim,igtf-policy-bundle,spl-linux
configure.ac	boinc,cockpit,erlang-p1-iconv,erlang-p1-pam,erlang-p1-sip,erlang-p1-stringprep,erlang-p1-tls,erlang-p1-xml,erlang-p1-yaml,erlang-p1-zlib,gajim,libsodium,mash,shadowsocks-libev,simple-obfs,spl-linux
.
16718a
config.rpath	erlang-p1-iconv
config.sub	erlang-p1-iconv
.
16717a
config.guess	erlang-p1-iconv
.
16657a
compile	erlang-p1-iconv
.
16650a
clstr2tree.pl	cd-hit
clstr2txt.pl	cd-hit
clstr2xml.pl	cd-hit
clstr_cut.pl	cd-hit
clstr_list.pl	cd-hit
clstr_list_sort.pl	cd-hit
clstr_merge.pl	cd-hit
clstr_merge_noorder.pl	cd-hit
clstr_quality_eval.pl	cd-hit
clstr_quality_eval_by_link.pl	cd-hit
clstr_reduce.pl	cd-hit
clstr_renumber.pl	cd-hit
clstr_rep.pl	cd-hit
clstr_reps_faa_rev.pl	cd-hit
clstr_rev.pl	cd-hit
clstr_select.pl	cd-hit
clstr_select_rep.pl	cd-hit
clstr_size_histogram.pl	cd-hit
clstr_size_stat.pl	cd-hit
clstr_sort_by.pl	cd-hit
clstr_sort_prot_by.pl	cd-hit
clstr_sql_tbl.pl	cd-hit
clstr_sql_tbl_sort.pl	cd-hit
.
15730a
c_src/decoder.c	erlang-jiffy
c_src/double-conversion/AUTHORS	erlang-jiffy
c_src/double-conversion/COPYING	erlang-jiffy
c_src/double-conversion/LICENSE	erlang-jiffy
c_src/double-conversion/README	erlang-jiffy
c_src/double-conversion/VERSION	erlang-jiffy
c_src/double-conversion/bignum-dtoa.cc	erlang-jiffy
c_src/double-conversion/bignum-dtoa.h	erlang-jiffy
c_src/double-conversion/bignum.cc	erlang-jiffy
c_src/double-conversion/bignum.h	erlang-jiffy
c_src/double-conversion/cached-powers.cc	erlang-jiffy
c_src/double-conversion/cached-powers.h	erlang-jiffy
c_src/double-conversion/diy-fp.cc	erlang-jiffy
c_src/double-conversion/diy-fp.h	erlang-jiffy
c_src/double-conversion/double-conversion.cc	erlang-jiffy
c_src/double-conversion/double-conversion.h	erlang-jiffy
c_src/double-conversion/fast-dtoa.cc	erlang-jiffy
c_src/double-conversion/fast-dtoa.h	erlang-jiffy
c_src/double-conversion/fixed-dtoa.cc	erlang-jiffy
c_src/double-conversion/fixed-dtoa.h	erlang-jiffy
c_src/double-conversion/ieee.h	erlang-jiffy
c_src/double-conversion/strtod.cc	erlang-jiffy
c_src/double-conversion/strtod.h	erlang-jiffy
c_src/double-conversion/utils.h	erlang-jiffy
c_src/doubles.cc	erlang-jiffy
c_src/encoder.c	erlang-jiffy
c_src/epam.c	erlang-p1-pam
c_src/esip_codec.c	erlang-p1-sip
c_src/ets_cache.c	erlang-p1-cache-tab
c_src/ezlib_drv.c	erlang-p1-zlib
c_src/fast_tls.c	erlang-p1-tls
c_src/fast_yaml.c	erlang-p1-yaml
c_src/fxml.c	erlang-p1-xml
c_src/fxml_stream.c	erlang-p1-xml
c_src/hashmap.c	erlang-p1-tls
c_src/hashmap.h	erlang-p1-tls
c_src/iconv.c	erlang-p1-iconv
c_src/jid.c	erlang-p1-xmpp
c_src/jiffy.c	erlang-jiffy
c_src/jiffy.h	erlang-jiffy
c_src/options.h	erlang-p1-tls
c_src/p1_sha.c	erlang-p1-tls
c_src/stdint.h	erlang-p1-tls
c_src/stringprep.cpp	erlang-p1-stringprep
c_src/uni_data.c	erlang-p1-stringprep
c_src/uni_norm.c	erlang-p1-stringprep
c_src/utf8.c	erlang-jiffy
c_src/util.c	erlang-jiffy
cd-hit-2d-para.pl	cd-hit
cd-hit-auxtools/Makefile	cd-hit
cd-hit-auxtools/bioSequence.cxx	cd-hit
cd-hit-auxtools/bioSequence.hxx	cd-hit
cd-hit-auxtools/cd-hit-dup-PE-out.pl	cd-hit
cd-hit-auxtools/cdhit-dup.cxx	cd-hit
cd-hit-auxtools/cdhit-lap.cxx	cd-hit
cd-hit-auxtools/mintlib/minArray.hxx	cd-hit
cd-hit-auxtools/mintlib/minBase.hxx	cd-hit
cd-hit-auxtools/mintlib/minMap.cxx	cd-hit
cd-hit-auxtools/mintlib/minMap.hxx	cd-hit
cd-hit-auxtools/mintlib/minString.cxx	cd-hit
cd-hit-auxtools/mintlib/minString.hxx	cd-hit
cd-hit-auxtools/mintlib/minUtility.hxx	cd-hit
cd-hit-auxtools/read-linker.cxx	cd-hit
cd-hit-div.pl	cd-hit
cd-hit-para.pl	cd-hit
cdhit-2d.c++	cd-hit
cdhit-454.c++	cd-hit
cdhit-common.c++	cd-hit
cdhit-common.h	cd-hit
cdhit-div.c++	cd-hit
cdhit-est-2d.c++	cd-hit
cdhit-est.c++	cd-hit
cdhit-utility.c++	cd-hit
cdhit-utility.h	cd-hit
cdhit.c++	cd-hit
.
15661a
bootstrap.sh	mash
bseq.c	fermi-lite,minimap
bseq.h	minimap
bubble.c	fermi-lite
.
15642a
bfc.c	fermi-lite
bfc.h	fermi-lite
.
15641a
ariba/__init__.py	ariba
ariba/aln_to_metadata.py	ariba
ariba/assembly.py	ariba
ariba/assembly_compare.py	ariba
ariba/assembly_variants.py	ariba
ariba/bam_parse.py	ariba
ariba/card_record.py	ariba
ariba/cdhit.py	ariba
ariba/cluster.py	ariba
ariba/clusters.py	ariba
ariba/common.py	ariba
ariba/ext/fml-asm_ariba.cpp	ariba
ariba/ext/minimap_ariba.cpp	ariba
ariba/ext/vcfcall_ariba.cpp	ariba
ariba/external_progs.py	ariba
ariba/faidx.py	ariba
ariba/flag.py	ariba
ariba/histogram.py	ariba
ariba/link.py	ariba
ariba/mapping.py	ariba
ariba/megares_data_finder.py	ariba
ariba/megares_zip_parser.py	ariba
ariba/mic_plotter.py	ariba
ariba/mlst_profile.py	ariba
ariba/mlst_reporter.py	ariba
ariba/pubmlst_getter.py	ariba
ariba/pubmlst_ref_preparer.py	ariba
ariba/read_filter.py	ariba
ariba/read_store.py	ariba
ariba/ref_genes_getter.py	ariba
ariba/ref_preparer.py	ariba
ariba/ref_seq_chooser.py	ariba
ariba/refdata_query.py	ariba
ariba/reference_data.py	ariba
ariba/report.py	ariba
ariba/report_filter.py	ariba
ariba/report_flag_expander.py	ariba
ariba/samtools_variants.py	ariba
ariba/scaffold_graph.py	ariba
ariba/sequence_metadata.py	ariba
ariba/sequence_variant.py	ariba
ariba/summary.py	ariba
ariba/summary_cluster.py	ariba
ariba/summary_cluster_variant.py	ariba
ariba/summary_sample.py	ariba
ariba/tasks/__init__.py	ariba
ariba/tasks/aln2meta.py	ariba
ariba/tasks/expandflag.py	ariba
ariba/tasks/flag.py	ariba
ariba/tasks/getref.py	ariba
ariba/tasks/micplot.py	ariba
ariba/tasks/prepareref.py	ariba
ariba/tasks/pubmlstget.py	ariba
ariba/tasks/pubmlstspecies.py	ariba
ariba/tasks/refquery.py	ariba
ariba/tasks/reportfilter.py	ariba
ariba/tasks/run.py	ariba
ariba/tasks/summary.py	ariba
ariba/tasks/test.py	ariba
ariba/tasks/version.py	ariba
ariba/test_run_data/metadata.tsv	ariba
ariba/test_run_data/reads_1.fq	ariba
ariba/test_run_data/reads_2.fq	ariba
ariba/test_run_data/ref_fasta_to_make_reads_from.fa	ariba
ariba/test_run_data/ref_seqs.fa	ariba
ariba/tests/aln_to_metadata_test.py	ariba
ariba/tests/assembly_compare_test.py	ariba
ariba/tests/assembly_test.py	ariba
ariba/tests/assembly_variants_test.py	ariba
ariba/tests/bam_parse_test.py	ariba
ariba/tests/card_record_test.py	ariba
ariba/tests/cdhit_test.py	ariba
ariba/tests/cluster_test.py	ariba
ariba/tests/clusters_test.py	ariba
ariba/tests/common_test.py	ariba
ariba/tests/data/aln_to_metadata_load_aln_file.in.fa	ariba
ariba/tests/data/aln_to_metadata_load_vars_file_bad.1.tsv	ariba
ariba/tests/data/aln_to_metadata_load_vars_file_bad.2.tsv	ariba
ariba/tests/data/aln_to_metadata_load_vars_file_good.tsv	ariba
ariba/tests/data/aln_to_metadata_make_cluster_file.out	ariba
ariba/tests/data/aln_to_metadata_run_coding.in.fa	ariba
ariba/tests/data/aln_to_metadata_run_coding.in.tsv	ariba
ariba/tests/data/aln_to_metadata_run_coding.out.cluster	ariba
ariba/tests/data/aln_to_metadata_run_coding.out.fa	ariba
ariba/tests/data/aln_to_metadata_run_coding.out.tsv	ariba
ariba/tests/data/aln_to_metadata_run_noncoding.in.fa	ariba
ariba/tests/data/aln_to_metadata_run_noncoding.in.tsv	ariba
ariba/tests/data/aln_to_metadata_run_noncoding.out.cluster	ariba
ariba/tests/data/aln_to_metadata_run_noncoding.out.fa	ariba
ariba/tests/data/aln_to_metadata_run_noncoding.out.tsv	ariba
ariba/tests/data/assembly_assemble_with_fermilite.expected.fa	ariba
ariba/tests/data/assembly_assemble_with_fermilite.expected.log	ariba
ariba/tests/data/assembly_assemble_with_fermilite.reads_1.fq	ariba
ariba/tests/data/assembly_assemble_with_fermilite.reads_2.fq	ariba
ariba/tests/data/assembly_assemble_with_fermilite_fails.expected.log	ariba
ariba/tests/data/assembly_assemble_with_fermilite_fails.reads_1.fq	ariba
ariba/tests/data/assembly_assemble_with_fermilite_fails.reads_2.fq	ariba
ariba/tests/data/assembly_compare_parse_nucmer_coords_file.coords	ariba
ariba/tests/data/assembly_run_fermilite.expected.fa	ariba
ariba/tests/data/assembly_run_fermilite.expected.log	ariba
ariba/tests/data/assembly_run_fermilite.reads.fq	ariba
ariba/tests/data/assembly_run_fermilite_fail.reads.fq	ariba
ariba/tests/data/assembly_run_fermilite_fails.expected.log	ariba
ariba/tests/data/assembly_test_fix_contig_orientation.in.fa	ariba
ariba/tests/data/assembly_test_fix_contig_orientation.out.fa	ariba
ariba/tests/data/assembly_test_fix_contig_orientation.ref.fa	ariba
ariba/tests/data/assembly_test_parse_assembly_bam.assembly.fa	ariba
ariba/tests/data/assembly_test_parse_assembly_bam.bam	ariba
ariba/tests/data/assembly_test_scaffold_with_sspace_contigs.fa	ariba
ariba/tests/data/assembly_test_scaffold_with_sspace_reads_1.fq	ariba
ariba/tests/data/assembly_test_scaffold_with_sspace_reads_2.fq	ariba
ariba/tests/data/assembly_variants_one_var_one_ctg_cdg.fa	ariba
ariba/tests/data/assembly_variants_one_var_one_ctg_cdg.tsv	ariba
ariba/tests/data/assembly_variants_one_var_one_ctg_noncdg.fa	ariba
ariba/tests/data/assembly_variants_one_var_one_ctg_noncdg.tsv	ariba
ariba/tests/data/assembly_variants_test_get_mummer_variants.none.snps	ariba
ariba/tests/data/assembly_variants_test_get_mummer_variants.snp.snps	ariba
ariba/tests/data/assembly_variants_test_get_variants_presence_absence.fa	ariba
ariba/tests/data/assembly_variants_test_get_variants_presence_absence.snps	ariba
ariba/tests/data/assembly_variants_test_get_variants_variants_only.fa	ariba
ariba/tests/data/assembly_variants_test_get_variants_variants_only.snps	ariba
ariba/tests/data/bam_parse_test_parse.bam	ariba
ariba/tests/data/bam_parse_test_parse.reads_1.fq	ariba
ariba/tests/data/bam_parse_test_parse.reads_2.fq	ariba
ariba/tests/data/bam_parse_test_parse.ref.fa	ariba
ariba/tests/data/bam_parse_test_sam_to_soft_clipped.bam	ariba
ariba/tests/data/bam_parse_test_sam_to_soft_clipped.reads.fq	ariba
ariba/tests/data/bam_parse_test_sam_to_soft_clipped.ref.fa	ariba
ariba/tests/data/bam_parse_test_update_soft_clipped_from_sam.bam	ariba
ariba/tests/data/bam_parse_test_update_soft_clipped_from_sam.reads.fq	ariba
ariba/tests/data/bam_parse_test_update_soft_clipped_from_sam.ref.fa	ariba
ariba/tests/data/bam_parse_test_update_unmapped_mates_from_sam.bam	ariba
ariba/tests/data/bam_parse_test_update_unmapped_mates_from_sam.reads_1.fq	ariba
ariba/tests/data/bam_parse_test_update_unmapped_mates_from_sam.reads_2.fq	ariba
ariba/tests/data/bam_parse_test_update_unmapped_mates_from_sam.ref.fa	ariba
ariba/tests/data/best_seq_chooser_best_seq_reads_1.fq	ariba
ariba/tests/data/best_seq_chooser_best_seq_reads_2.fq	ariba
ariba/tests/data/best_seq_chooser_best_seq_ref.fa	ariba
ariba/tests/data/best_seq_chooser_best_seq_ref.fa.fai	ariba
ariba/tests/data/best_seq_chooser_get_best_seq_by_alignment_score_reads_1.fq	ariba
ariba/tests/data/best_seq_chooser_get_best_seq_by_alignment_score_reads_2.fq	ariba
ariba/tests/data/best_seq_chooser_get_best_seq_by_alignment_score_ref.fa	ariba
ariba/tests/data/best_seq_chooser_get_best_seq_by_alignment_score_ref.fa.fai	ariba
ariba/tests/data/best_seq_chooser_total_alignment_score_reads_1.fq	ariba
ariba/tests/data/best_seq_chooser_total_alignment_score_reads_2.fq	ariba
ariba/tests/data/best_seq_chooser_total_alignment_score_ref_seqs.fa	ariba
ariba/tests/data/best_seq_chooser_total_alignment_score_ref_seqs.fa.fai	ariba
ariba/tests/data/cdhit_test_fake_run.in.fa	ariba
ariba/tests/data/cdhit_test_fake_run.non-unique.in.fa	ariba
ariba/tests/data/cdhit_test_get_clusters_from_bak_file.in	ariba
ariba/tests/data/cdhit_test_load_user_clusters_file.bad1	ariba
ariba/tests/data/cdhit_test_load_user_clusters_file.bad2	ariba
ariba/tests/data/cdhit_test_load_user_clusters_file.bad3	ariba
ariba/tests/data/cdhit_test_load_user_clusters_file.good	ariba
ariba/tests/data/cdhit_test_run.in.fa	ariba
ariba/tests/data/cdhit_test_run_get_clusters_from_dict.in.clusters	ariba
ariba/tests/data/cdhit_test_run_get_clusters_from_dict.in.fa	ariba
ariba/tests/data/cdhit_test_run_get_clusters_from_dict_rename.in.fa	ariba
ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_gene.fa	ariba
ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_gene.ref_for_reads.fa	ariba
ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_gene.tsv	ariba
ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_gene/reads_1.fq	ariba
ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_gene/reads_2.fq	ariba
ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_gene/references.fa	ariba
ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_nonc.fa	ariba
ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_nonc.tsv	ariba
ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_nonc/reads_1.fq	ariba
ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_nonc/reads_2.fq	ariba
ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_nonc/references.fa	ariba
ariba/tests/data/cluster_full_run_smtls_known_snp_presabs_nonc.fa	ariba
ariba/tests/data/cluster_full_run_smtls_known_snp_presabs_nonc.tsv	ariba
ariba/tests/data/cluster_full_run_smtls_known_snp_presabs_nonc/reads_1.fq	ariba
ariba/tests/data/cluster_full_run_smtls_known_snp_presabs_nonc/reads_2.fq	ariba
ariba/tests/data/cluster_full_run_smtls_known_snp_presabs_nonc/references.fa	ariba
ariba/tests/data/cluster_full_run_smtls_snp_presabs_gene.fa	ariba
ariba/tests/data/cluster_full_run_smtls_snp_presabs_gene.ref_for_reads.fa	ariba
ariba/tests/data/cluster_full_run_smtls_snp_presabs_gene.tsv	ariba
ariba/tests/data/cluster_full_run_smtls_snp_presabs_gene/reads_1.fq	ariba
ariba/tests/data/cluster_full_run_smtls_snp_presabs_gene/reads_2.fq	ariba
ariba/tests/data/cluster_full_run_smtls_snp_presabs_gene/references.fa	ariba
ariba/tests/data/cluster_full_run_smtls_snp_presabs_nonc.fa	ariba
ariba/tests/data/cluster_full_run_smtls_snp_presabs_nonc.tsv	ariba
ariba/tests/data/cluster_full_run_smtls_snp_presabs_nonc/reads_1.fq	ariba
ariba/tests/data/cluster_full_run_smtls_snp_presabs_nonc/reads_2.fq	ariba
ariba/tests/data/cluster_full_run_smtls_snp_presabs_nonc/references.fa	ariba
ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene.fa	ariba
ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene.tsv	ariba
ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene/reads_1.fq	ariba
ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene/reads_2.fq	ariba
ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene/references.fa	ariba
ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_2.fa	ariba
ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_2.tsv	ariba
ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_2/reads_1.fq	ariba
ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_2/reads_2.fq	ariba
ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_2/references.fa	ariba
ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_no_snp.fa	ariba
ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_no_snp.tsv	ariba
ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_no_snp/reads_1.fq	ariba
ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_no_snp/reads_2.fq	ariba
ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_no_snp/references.fa	ariba
ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc.fa	ariba
ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc.tsv	ariba
ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc/reads_1.fq	ariba
ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc/reads_2.fq	ariba
ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc/references.fa	ariba
ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc_no_snp.fa	ariba
ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc_no_snp.tsv	ariba
ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc_no_snp/reads_1.fq	ariba
ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc_no_snp/reads_2.fq	ariba
ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc_no_snp/references.fa	ariba
ariba/tests/data/cluster_full_run_varonly.not_present.always_report.tsv	ariba
ariba/tests/data/cluster_test_count_reads_1.fq	ariba
ariba/tests/data/cluster_test_count_reads_2.fq	ariba
ariba/tests/data/cluster_test_full_run_assembly_fail.in.fa	ariba
ariba/tests/data/cluster_test_full_run_assembly_fail.in.tsv	ariba
ariba/tests/data/cluster_test_full_run_assembly_fail/reads_1.fq	ariba
ariba/tests/data/cluster_test_full_run_assembly_fail/reads_2.fq	ariba
ariba/tests/data/cluster_test_full_run_assembly_fail/references.fa	ariba
ariba/tests/data/cluster_test_full_run_choose_ref_fail.in.fa	ariba
ariba/tests/data/cluster_test_full_run_choose_ref_fail.in.tsv	ariba
ariba/tests/data/cluster_test_full_run_choose_ref_fail/reads_1.fq	ariba
ariba/tests/data/cluster_test_full_run_choose_ref_fail/reads_2.fq	ariba
ariba/tests/data/cluster_test_full_run_choose_ref_fail/references.fa	ariba
ariba/tests/data/cluster_test_full_run_delete_codon.fa	ariba
ariba/tests/data/cluster_test_full_run_delete_codon.tsv	ariba
ariba/tests/data/cluster_test_full_run_delete_codon/for_reads.fa	ariba
ariba/tests/data/cluster_test_full_run_delete_codon/reads_1.fq	ariba
ariba/tests/data/cluster_test_full_run_delete_codon/reads_2.fq	ariba
ariba/tests/data/cluster_test_full_run_delete_codon/references.fa	ariba
ariba/tests/data/cluster_test_full_run_insert_codon.fa	ariba
ariba/tests/data/cluster_test_full_run_insert_codon.tsv	ariba
ariba/tests/data/cluster_test_full_run_insert_codon/for_reads.fa	ariba
ariba/tests/data/cluster_test_full_run_insert_codon/reads_1.fq	ariba
ariba/tests/data/cluster_test_full_run_insert_codon/reads_2.fq	ariba
ariba/tests/data/cluster_test_full_run_insert_codon/references.fa	ariba
ariba/tests/data/cluster_test_full_run_multiple_vars.fa	ariba
ariba/tests/data/cluster_test_full_run_multiple_vars.tsv	ariba
ariba/tests/data/cluster_test_full_run_multiple_vars/for_reads.fa	ariba
ariba/tests/data/cluster_test_full_run_multiple_vars/reads_1.fq	ariba
ariba/tests/data/cluster_test_full_run_multiple_vars/reads_2.fq	ariba
ariba/tests/data/cluster_test_full_run_multiple_vars/references.fa	ariba
ariba/tests/data/cluster_test_full_run_no_reads_after_filtering.in.fa	ariba
ariba/tests/data/cluster_test_full_run_no_reads_after_filtering.in.tsv	ariba
ariba/tests/data/cluster_test_full_run_no_reads_after_filtering/reads_1.fq	ariba
ariba/tests/data/cluster_test_full_run_no_reads_after_filtering/reads_2.fq	ariba
ariba/tests/data/cluster_test_full_run_no_reads_after_filtering/references.fa	ariba
ariba/tests/data/cluster_test_full_run_ok_gene_start_mismatch.fa	ariba
ariba/tests/data/cluster_test_full_run_ok_gene_start_mismatch.metadata.tsv	ariba
ariba/tests/data/cluster_test_full_run_ok_gene_start_mismatch.ref_for_reads.fa	ariba
ariba/tests/data/cluster_test_full_run_ok_gene_start_mismatch/reads_1.fq	ariba
ariba/tests/data/cluster_test_full_run_ok_gene_start_mismatch/reads_2.fq	ariba
ariba/tests/data/cluster_test_full_run_ok_gene_start_mismatch/references.fa	ariba
ariba/tests/data/cluster_test_full_run_ok_non_coding.fa	ariba
ariba/tests/data/cluster_test_full_run_ok_non_coding.metadata.tsv	ariba
ariba/tests/data/cluster_test_full_run_ok_non_coding/reads_1.fq	ariba
ariba/tests/data/cluster_test_full_run_ok_non_coding/reads_2.fq	ariba
ariba/tests/data/cluster_test_full_run_ok_non_coding/references.fa	ariba
ariba/tests/data/cluster_test_full_run_ok_presence_absence.fa	ariba
ariba/tests/data/cluster_test_full_run_ok_presence_absence.metadata.tsv	ariba
ariba/tests/data/cluster_test_full_run_ok_presence_absence/reads_1.fq	ariba
ariba/tests/data/cluster_test_full_run_ok_presence_absence/reads_2.fq	ariba
ariba/tests/data/cluster_test_full_run_ok_presence_absence/references.fa	ariba
ariba/tests/data/cluster_test_full_run_ok_variants_only.fa	ariba
ariba/tests/data/cluster_test_full_run_ok_variants_only.not_present.metadata.tsv	ariba
ariba/tests/data/cluster_test_full_run_ok_variants_only.present.metadata.tsv	ariba
ariba/tests/data/cluster_test_full_run_ok_variants_only/reads_1.fq	ariba
ariba/tests/data/cluster_test_full_run_ok_variants_only/reads_2.fq	ariba
ariba/tests/data/cluster_test_full_run_ok_variants_only/references.fa	ariba
ariba/tests/data/cluster_test_full_run_partial_asmbly.fa	ariba
ariba/tests/data/cluster_test_full_run_partial_asmbly.tsv	ariba
ariba/tests/data/cluster_test_full_run_partial_asmbly/reads_1.fq	ariba
ariba/tests/data/cluster_test_full_run_partial_asmbly/reads_2.fq	ariba
ariba/tests/data/cluster_test_full_run_partial_asmbly/references.fa	ariba
ariba/tests/data/cluster_test_full_run_ref_not_in_cluster.all_refs.fa	ariba
ariba/tests/data/cluster_test_full_run_ref_not_in_cluster.in.fa	ariba
ariba/tests/data/cluster_test_full_run_ref_not_in_cluster.in.tsv	ariba
ariba/tests/data/cluster_test_full_run_ref_not_in_cluster/reads_1.fq	ariba
ariba/tests/data/cluster_test_full_run_ref_not_in_cluster/reads_2.fq	ariba
ariba/tests/data/cluster_test_full_run_ref_not_in_cluster/references.fa	ariba
ariba/tests/data/cluster_test_full_run_smtls_snp_varonly_nonc.fa	ariba
ariba/tests/data/cluster_test_full_run_smtls_snp_varonly_nonc.tsv	ariba
ariba/tests/data/cluster_test_full_run_smtls_snp_varonly_nonc/reads_1.fq	ariba
ariba/tests/data/cluster_test_full_run_smtls_snp_varonly_nonc/reads_2.fq	ariba
ariba/tests/data/cluster_test_full_run_smtls_snp_varonly_nonc/references.fa	ariba
ariba/tests/data/cluster_test_init_no_reads_1/genes.fa	ariba
ariba/tests/data/cluster_test_init_no_reads_1/reads_2.fq	ariba
ariba/tests/data/cluster_test_init_no_reads_2/genes.fa	ariba
ariba/tests/data/cluster_test_init_no_reads_2/reads_1.fq	ariba
ariba/tests/data/cluster_test_init_no_refs_fa/reads_1.fq	ariba
ariba/tests/data/cluster_test_init_no_refs_fa/reads_2.fq	ariba
ariba/tests/data/cluster_test_init_refdata.fa	ariba
ariba/tests/data/cluster_test_init_refdata.tsv	ariba
ariba/tests/data/cluster_test_make_reads_for_assembly.in1.fq	ariba
ariba/tests/data/cluster_test_make_reads_for_assembly.in2.fq	ariba
ariba/tests/data/cluster_test_make_reads_for_assembly.out1.fq	ariba
ariba/tests/data/cluster_test_make_reads_for_assembly.out2.fq	ariba
ariba/tests/data/clusters_cat_genes_match_ref.fa	ariba
ariba/tests/data/clusters_load_ref_data_from_dir/00.info.txt	ariba
ariba/tests/data/clusters_load_ref_data_from_dir/01.filter.check_metadata.tsv	ariba
ariba/tests/data/clusters_load_ref_data_from_dir/02.cdhit.all.fa	ariba
ariba/tests/data/clusters_load_ref_data_from_dir/02.cdhit.clusters.pickle	ariba
ariba/tests/data/clusters_minimap_reads_to_all_refs.clstrs.tsv	ariba
ariba/tests/data/clusters_minimap_reads_to_all_refs.out.clstr2rep	ariba
ariba/tests/data/clusters_minimap_reads_to_all_refs.out.clstr_count	ariba
ariba/tests/data/clusters_minimap_reads_to_all_refs.out.hist	ariba
ariba/tests/data/clusters_minimap_reads_to_all_refs.out.pairs	ariba
ariba/tests/data/clusters_minimap_reads_to_all_refs.reads_1.fq	ariba
ariba/tests/data/clusters_minimap_reads_to_all_refs.reads_2.fq	ariba
ariba/tests/data/clusters_minimap_reads_to_all_refs.ref.fa	ariba
ariba/tests/data/clusters_test_bam_to_clusters_reads.db.fa.fai	ariba
ariba/tests/data/clusters_test_bam_to_clusters_reads.db.fa.sma	ariba
ariba/tests/data/clusters_test_bam_to_clusters_reads.db.fa.smi	ariba
ariba/tests/data/clusters_test_dummy_db.fa	ariba
ariba/tests/data/clusters_test_dummy_db.tsv	ariba
ariba/tests/data/clusters_test_dummy_reads_1.fq	ariba
ariba/tests/data/clusters_test_dummy_reads_2.fq	ariba
ariba/tests/data/clusters_test_load_data_info_file	ariba
ariba/tests/data/clusters_test_load_minimap_files.cluster2representative	ariba
ariba/tests/data/clusters_test_load_minimap_files.clusterCounts	ariba
ariba/tests/data/clusters_test_load_minimap_files.insertHistogram	ariba
ariba/tests/data/clusters_test_load_minimap_files.properPairs	ariba
ariba/tests/data/clusters_test_load_minimap_insert_histogram.in	ariba
ariba/tests/data/clusters_test_load_minimap_out_cluster2representative.in	ariba
ariba/tests/data/clusters_test_load_minimap_out_cluster_counts.in	ariba
ariba/tests/data/clusters_test_load_minimap_proper_pairs.in	ariba
ariba/tests/data/clusters_test_sam_pair_to_insert_reads_1.fq	ariba
ariba/tests/data/clusters_test_sam_pair_to_insert_reads_2.fq	ariba
ariba/tests/data/clusters_test_sam_pair_to_insert_ref.fa	ariba
ariba/tests/data/clusters_test_sam_pair_to_insert_ref.fa.sma	ariba
ariba/tests/data/clusters_test_sam_pair_to_insert_ref.fa.smi	ariba
ariba/tests/data/clusters_test_write_catted_assembled_genes_fasta.expected.out.fa	ariba
ariba/tests/data/clusters_test_write_catted_assemblies_fasta.expected.out.fa	ariba
ariba/tests/data/clusters_test_write_gene_fa.db.fa	ariba
ariba/tests/data/clusters_test_write_gene_fa.db.fa.fai	ariba
ariba/tests/data/clusters_test_write_gene_fa.out.fa	ariba
ariba/tests/data/clusters_test_write_mlst_reports.ariba.report.tsv	ariba
ariba/tests/data/clusters_test_write_mlst_reports.mlst_profile.tsv	ariba
ariba/tests/data/clusters_test_write_mlst_reports.out.details.tsv	ariba
ariba/tests/data/clusters_test_write_mlst_reports.out.tsv	ariba
ariba/tests/data/clusters_test_write_report.tsv	ariba
ariba/tests/data/dummy.bam	ariba
ariba/tests/data/faidx_test_write_fa_subset.in.fa	ariba
ariba/tests/data/faidx_test_write_fa_subset.in.fa.fai	ariba
ariba/tests/data/faidx_test_write_fa_subset.out.fa	ariba
ariba/tests/data/graph_test_update_from_sam.bam	ariba
ariba/tests/data/graph_test_update_from_sam.reads_1.fq	ariba
ariba/tests/data/graph_test_update_from_sam.reads_2.fq	ariba
ariba/tests/data/graph_test_update_from_sam.ref.fa	ariba
ariba/tests/data/graph_test_update_from_sam.ref.fa.fai	ariba
ariba/tests/data/graph_test_write_all_links_to_file.out	ariba
ariba/tests/data/link_test_init.reads.make_link.bam	ariba
ariba/tests/data/link_test_init.reads.make_link.bam.bai	ariba
ariba/tests/data/link_test_init.reads.make_link_1.fq	ariba
ariba/tests/data/link_test_init.reads.make_link_2.fq	ariba
ariba/tests/data/link_test_init.reads.no_link.bam	ariba
ariba/tests/data/link_test_init.reads.no_link.bam.bai	ariba
ariba/tests/data/link_test_init.reads.no_link_1.fq	ariba
ariba/tests/data/link_test_init.reads.no_link_2.fq	ariba
ariba/tests/data/link_test_init.reads_1.fq	ariba
ariba/tests/data/link_test_init.reads_2.fq	ariba
ariba/tests/data/link_test_init.ref.fa	ariba
ariba/tests/data/link_test_init.ref.fa.fai	ariba
ariba/tests/data/mapping_test_bowtie2_reads_1.fq	ariba
ariba/tests/data/mapping_test_bowtie2_reads_2.fq	ariba
ariba/tests/data/mapping_test_bowtie2_ref.fa	ariba
ariba/tests/data/mapping_test_bowtie2_ref.fa.fai	ariba
ariba/tests/data/mapping_test_bowtie2_remove_both_unmapped_reads.bam	ariba
ariba/tests/data/mapping_test_bowtie2_remove_both_unmapped_reads_1.fq	ariba
ariba/tests/data/mapping_test_bowtie2_remove_both_unmapped_reads_2.fq	ariba
ariba/tests/data/mapping_test_bowtie2_sorted.bam	ariba
ariba/tests/data/mapping_test_bowtie2_unsorted.bam	ariba
ariba/tests/data/mapping_test_get_total_alignment_score.bam	ariba
ariba/tests/data/mapping_test_sam_pair_to_insert.bam	ariba
ariba/tests/data/mapping_test_sam_to_fastq.bam	ariba
ariba/tests/data/megares_zip_parse_extract_files_ok.zip	ariba
ariba/tests/data/megares_zip_parse_extract_files_one_missing.zip	ariba
ariba/tests/data/megares_zip_parser_load_annotations.csv	ariba
ariba/tests/data/megares_zip_parser_load_header_mappings.tsv	ariba
ariba/tests/data/megares_zip_parser_write_files.expect.fa	ariba
ariba/tests/data/megares_zip_parser_write_files.expect.tsv	ariba
ariba/tests/data/megares_zip_parser_write_files/megares_annotations_v1.01.csv	ariba
ariba/tests/data/megares_zip_parser_write_files/megares_database_v1.01.fasta	ariba
ariba/tests/data/megares_zip_parser_write_files/megares_to_external_header_mappings_v1.01.tsv	ariba
ariba/tests/data/mic_plotter_load_mic_file.tsv	ariba
ariba/tests/data/mic_plotter_load_summary_file.tsv	ariba
ariba/tests/data/mic_plotter_to_boxplot_tsv.antibio1.exclude.no_combinations.tsv	ariba
ariba/tests/data/mic_plotter_to_boxplot_tsv.antibio1.exclude.tsv	ariba
ariba/tests/data/mic_plotter_to_boxplot_tsv.antibio1.no.no_combinations.tsv	ariba
ariba/tests/data/mic_plotter_to_boxplot_tsv.antibio1.no.tsv	ariba
ariba/tests/data/mic_plotter_to_boxplot_tsv.antibio1.yes.no_combinations.tsv	ariba
ariba/tests/data/mic_plotter_to_boxplot_tsv.antibio1.yes.tsv	ariba
ariba/tests/data/mic_plotter_to_boxplot_tsv.antibio2.exclude.no_combinations.tsv	ariba
ariba/tests/data/mic_plotter_to_boxplot_tsv.antibio2.exclude.tsv	ariba
ariba/tests/data/mic_plotter_to_boxplot_tsv.antibio2.no.no_combinations.tsv	ariba
ariba/tests/data/mic_plotter_to_boxplot_tsv.antibio2.no.tsv	ariba
ariba/tests/data/mic_plotter_to_boxplot_tsv.antibio2.yes.no_combinations.tsv	ariba
ariba/tests/data/mic_plotter_to_boxplot_tsv.antibio2.yes.tsv	ariba
ariba/tests/data/mlst_profile_test.init.profile.tsv	ariba
ariba/tests/data/mlst_profile_test.init_multiple_extra_columns.profile.tsv	ariba
ariba/tests/data/mlst_profile_test.profile.tsv	ariba
ariba/tests/data/mlst_reporter.all_present_perfect.report.in.tsv	ariba
ariba/tests/data/mlst_reporter.all_present_perfect.report.out.details.tsv	ariba
ariba/tests/data/mlst_reporter.all_present_perfect.report.out.tsv	ariba
ariba/tests/data/mlst_reporter.het_snp.in.tsv	ariba
ariba/tests/data/mlst_reporter.het_snp.out.details.tsv	ariba
ariba/tests/data/mlst_reporter.het_snp.out.tsv	ariba
ariba/tests/data/mlst_reporter.het_snps.in.tsv	ariba
ariba/tests/data/mlst_reporter.het_snps.out.details.tsv	ariba
ariba/tests/data/mlst_reporter.het_snps.out.tsv	ariba
ariba/tests/data/mlst_reporter.new_st.report.in.tsv	ariba
ariba/tests/data/mlst_reporter.new_st.report.out.details.tsv	ariba
ariba/tests/data/mlst_reporter.new_st.report.out.tsv	ariba
ariba/tests/data/mlst_reporter.one_gene_missing.in.tsv	ariba
ariba/tests/data/mlst_reporter.one_gene_missing.out.details.tsv	ariba
ariba/tests/data/mlst_reporter.one_gene_missing.out.tsv	ariba
ariba/tests/data/mlst_reporter.profile.in.tsv	ariba
ariba/tests/data/pubmlst_getter.dbases.xml	ariba
ariba/tests/data/pubmlst_ref_prepare.test_load_fa_and_clusters.expect.tsv	ariba
ariba/tests/data/pubmlst_ref_prepare.test_load_fa_and_clusters.in/gene1.tfa	ariba
ariba/tests/data/pubmlst_ref_prepare.test_load_fa_and_clusters.in/gene2.tfa	ariba
ariba/tests/data/pubmlst_ref_prepare.test_load_fa_and_clusters.in/profile.txt	ariba
ariba/tests/data/pubmlst_rename_seqs.expected.fa	ariba
ariba/tests/data/pubmlst_rename_seqs.in.fa	ariba
ariba/tests/data/read_filter_cdhit_clstr_to_reads.in.clstr	ariba
ariba/tests/data/read_filter_test_run.expected.reads_1.fq	ariba
ariba/tests/data/read_filter_test_run.expected.reads_2.fq	ariba
ariba/tests/data/read_filter_test_run.in.read_store	ariba
ariba/tests/data/read_filter_test_run.in.reads_1.fq	ariba
ariba/tests/data/read_filter_test_run.in.reads_2.fq	ariba
ariba/tests/data/read_filter_test_run.in.ref.fa	ariba
ariba/tests/data/read_filter_test_run_cdhit_est_2d.expected.clstr	ariba
ariba/tests/data/read_filter_test_run_cdhit_est_2d.reads.in.fa	ariba
ariba/tests/data/read_filter_test_run_cdhit_est_2d.ref.in.fa	ariba
ariba/tests/data/read_store_test_clean.in	ariba
ariba/tests/data/read_store_test_compress_and_index_file.in	ariba
ariba/tests/data/read_store_test_get_reads.expected.reads.fa	ariba
ariba/tests/data/read_store_test_get_reads.expected.reads.fq	ariba
ariba/tests/data/read_store_test_get_reads.expected.reads_1.fa	ariba
ariba/tests/data/read_store_test_get_reads.expected.reads_1.fq	ariba
ariba/tests/data/read_store_test_get_reads.expected.reads_2.fa	ariba
ariba/tests/data/read_store_test_get_reads.expected.reads_2.fq	ariba
ariba/tests/data/read_store_test_get_reads.expected.reads_subset.1.fq	ariba
ariba/tests/data/read_store_test_get_reads.expected.reads_subset.2.fq	ariba
ariba/tests/data/read_store_test_get_reads.in	ariba
ariba/tests/data/read_store_test_sort_file.in	ariba
ariba/tests/data/read_store_test_sort_file.out	ariba
ariba/tests/data/ref_preparer_test_fasta_to_metadata.coding.tsv	ariba
ariba/tests/data/ref_preparer_test_fasta_to_metadata.fa	ariba
ariba/tests/data/ref_preparer_test_fasta_to_metadata.noncoding.tsv	ariba
ariba/tests/data/ref_preparer_test_run.in.1.fa	ariba
ariba/tests/data/ref_preparer_test_run.in.1.tsv	ariba
ariba/tests/data/ref_preparer_test_run.in.2.fa	ariba
ariba/tests/data/ref_preparer_test_run.in.2.tsv	ariba
ariba/tests/data/ref_preparer_test_run.in.3.fa	ariba
ariba/tests/data/ref_preparer_test_run.out/00.info.txt	ariba
ariba/tests/data/ref_preparer_test_run.out/00.version_info.txt	ariba
ariba/tests/data/ref_preparer_test_run.out/01.filter.check_genes.log	ariba
ariba/tests/data/ref_preparer_test_run.out/01.filter.check_metadata.log	ariba
ariba/tests/data/ref_preparer_test_run.out/01.filter.check_metadata.tsv	ariba
ariba/tests/data/ref_preparer_test_run.out/02.cdhit.all.fa	ariba
ariba/tests/data/ref_preparer_test_run.out/02.cdhit.clusters.pickle	ariba
ariba/tests/data/ref_preparer_test_run.out/02.cdhit.clusters.tsv	ariba
ariba/tests/data/ref_preparer_test_run.out/02.cdhit.gene.fa	ariba
ariba/tests/data/ref_preparer_test_run.out/02.cdhit.gene.varonly.fa	ariba
ariba/tests/data/ref_preparer_test_run.out/02.cdhit.noncoding.fa	ariba
ariba/tests/data/ref_preparer_test_run.out/02.cdhit.noncoding.varonly.fa	ariba
ariba/tests/data/ref_preparer_test_run_all_noncoding.out/00.auto_metadata.tsv	ariba
ariba/tests/data/ref_preparer_test_run_all_noncoding.out/00.info.txt	ariba
ariba/tests/data/ref_preparer_test_run_all_noncoding.out/00.version_info.txt	ariba
ariba/tests/data/ref_preparer_test_run_all_noncoding.out/01.filter.check_genes.log	ariba
ariba/tests/data/ref_preparer_test_run_all_noncoding.out/01.filter.check_metadata.log	ariba
ariba/tests/data/ref_preparer_test_run_all_noncoding.out/01.filter.check_metadata.tsv	ariba
ariba/tests/data/ref_preparer_test_run_all_noncoding.out/02.cdhit.all.fa	ariba
ariba/tests/data/ref_preparer_test_run_all_noncoding.out/02.cdhit.clusters.pickle	ariba
ariba/tests/data/ref_preparer_test_run_all_noncoding.out/02.cdhit.clusters.tsv	ariba
ariba/tests/data/ref_preparer_test_run_all_noncoding.out/02.cdhit.gene.fa	ariba
ariba/tests/data/ref_preparer_test_run_all_noncoding.out/02.cdhit.gene.varonly.fa	ariba
ariba/tests/data/ref_preparer_test_run_all_noncoding.out/02.cdhit.noncoding.fa	ariba
ariba/tests/data/ref_preparer_test_run_all_noncoding.out/02.cdhit.noncoding.varonly.fa	ariba
ariba/tests/data/ref_seq_chooser_full_run_best_match_is_in_cluster.allrefs.fa	ariba
ariba/tests/data/ref_seq_chooser_full_run_best_match_is_in_cluster.clusterrefs.fa	ariba
ariba/tests/data/ref_seq_chooser_full_run_best_match_is_in_cluster.contigs.fa	ariba
ariba/tests/data/ref_seq_chooser_full_run_best_match_not_in_cluster.allrefs.fa	ariba
ariba/tests/data/ref_seq_chooser_full_run_best_match_not_in_cluster.clusterrefs.fa	ariba
ariba/tests/data/ref_seq_chooser_full_run_best_match_not_in_cluster.contigs.fa	ariba
ariba/tests/data/ref_seq_chooser_full_run_contained_ref_seq.all_refs.fa	ariba
ariba/tests/data/ref_seq_chooser_full_run_contained_ref_seq.cluster_refs.fa	ariba
ariba/tests/data/ref_seq_chooser_full_run_contained_ref_seq.contigs.fa	ariba
ariba/tests/data/ref_seq_chooser_full_run_no_nucmer_match.allrefs.fa	ariba
ariba/tests/data/ref_seq_chooser_full_run_no_nucmer_match.clusterrefs.fa	ariba
ariba/tests/data/ref_seq_chooser_full_run_no_nucmer_match.contigs.fa	ariba
ariba/tests/data/ref_seq_chooser_full_run_not_in_cluster.allrefs.fa	ariba
ariba/tests/data/ref_seq_chooser_full_run_not_in_cluster.clusterrefs.fa	ariba
ariba/tests/data/ref_seq_chooser_full_run_not_in_cluster.contigs.fa	ariba
ariba/tests/data/ref_seq_chooser_matching_contig_pieces.coords	ariba
ariba/tests/data/ref_seq_chooser_matching_contig_pieces.ctg.fa	ariba
ariba/tests/data/ref_seq_chooser_matching_contig_pieces.expect.fa	ariba
ariba/tests/data/ref_seq_chooser_matching_contig_pieces.ref.fa	ariba
ariba/tests/data/ref_seq_chooser_sequence_is_in_fasta_file.fa	ariba
ariba/tests/data/ref_seq_chooser_test_flanking.all_refs.fa	ariba
ariba/tests/data/ref_seq_chooser_test_flanking.cluster_refs.fa	ariba
ariba/tests/data/ref_seq_chooser_test_flanking.contigs.fa	ariba
ariba/tests/data/ref_seq_chooser_test_flanking.expected_contigs.fa	ariba
ariba/tests/data/refcheck_test_check_duplicate_name.fa	ariba
ariba/tests/data/refcheck_test_check_not_gene.fa	ariba
ariba/tests/data/refcheck_test_check_ok.fa	ariba
ariba/tests/data/refcheck_test_check_spaces_in_name.fa	ariba
ariba/tests/data/refcheck_test_check_too_long.fa	ariba
ariba/tests/data/refcheck_test_check_too_short.fa	ariba
ariba/tests/data/refcheck_test_fix_in.fa	ariba
ariba/tests/data/refcheck_test_fix_out.fa	ariba
ariba/tests/data/refcheck_test_fix_out.log	ariba
ariba/tests/data/refcheck_test_fix_out.removed.fa	ariba
ariba/tests/data/refcheck_test_fix_out.rename	ariba
ariba/tests/data/refdata_query_prepareref.in.fa	ariba
ariba/tests/data/refdata_query_prepareref.in.tsv	ariba
ariba/tests/data/refdata_query_prepareref/00.info.txt	ariba
ariba/tests/data/refdata_query_prepareref/00.rename_info	ariba
ariba/tests/data/refdata_query_prepareref/00.version_info.txt	ariba
ariba/tests/data/refdata_query_prepareref/01.filter.check_genes.log	ariba
ariba/tests/data/refdata_query_prepareref/01.filter.check_metadata.log	ariba
ariba/tests/data/refdata_query_prepareref/01.filter.check_metadata.tsv	ariba
ariba/tests/data/refdata_query_prepareref/02.cdhit.all.fa	ariba
ariba/tests/data/refdata_query_prepareref/02.cdhit.clusters.pickle	ariba
ariba/tests/data/refdata_query_prepareref/02.cdhit.clusters.tsv	ariba
ariba/tests/data/refdata_query_prepareref/02.cdhit.gene.fa	ariba
ariba/tests/data/refdata_query_prepareref/02.cdhit.gene.varonly.fa	ariba
ariba/tests/data/refdata_query_prepareref/02.cdhit.noncoding.fa	ariba
ariba/tests/data/refdata_query_prepareref/02.cdhit.noncoding.varonly.fa	ariba
ariba/tests/data/reference_data_cluster_w_cdhit_clstrs_file.expect.clstrs.tsv	ariba
ariba/tests/data/reference_data_cluster_w_cdhit_clstrs_file.in.clstrs.tsv	ariba
ariba/tests/data/reference_data_cluster_w_cdhit_clstrs_file.in.fa	ariba
ariba/tests/data/reference_data_cluster_w_cdhit_clstrs_file.in.meta.tsv	ariba
ariba/tests/data/reference_data_cluster_w_cdhit_nocluster.expect.tsv	ariba
ariba/tests/data/reference_data_cluster_w_cdhit_nocluster.in.fa	ariba
ariba/tests/data/reference_data_cluster_w_cdhit_nocluster.in.tsv	ariba
ariba/tests/data/reference_data_filter_bad_data.expected.all.fa	ariba
ariba/tests/data/reference_data_filter_bad_data.expected.check_metadata.log	ariba
ariba/tests/data/reference_data_filter_bad_data.expected.check_metadata.tsv	ariba
ariba/tests/data/reference_data_filter_bad_data.expected.log	ariba
ariba/tests/data/reference_data_filter_bad_data.expected.metadata.tsv	ariba
ariba/tests/data/reference_data_filter_bad_data.in.fa	ariba
ariba/tests/data/reference_data_filter_bad_data_metadata.in.tsv	ariba
ariba/tests/data/reference_data_filter_bad_data_non_coding.in.fa	ariba
ariba/tests/data/reference_data_filter_bad_data_presence_absence.in.fa	ariba
ariba/tests/data/reference_data_filter_bad_data_variants_only.in.fa	ariba
ariba/tests/data/reference_data_init_fails.empty.fa	ariba
ariba/tests/data/reference_data_init_fails.empty.tsv	ariba
ariba/tests/data/reference_data_init_fails.in.fa	ariba
ariba/tests/data/reference_data_init_ok.in.fa	ariba
ariba/tests/data/reference_data_init_ok.in.tsv	ariba
ariba/tests/data/reference_data_init_ok.rename.tsv	ariba
ariba/tests/data/reference_data_keep_seqs_from_dict.fa	ariba
ariba/tests/data/reference_data_keep_seqs_from_dict.log	ariba
ariba/tests/data/reference_data_load_all_fasta_files.in.1	ariba
ariba/tests/data/reference_data_load_all_fasta_files.in.2	ariba
ariba/tests/data/reference_data_load_all_metadata_tsvs.1.tsv	ariba
ariba/tests/data/reference_data_load_all_metadata_tsvs.2.tsv	ariba
ariba/tests/data/reference_data_load_fasta_file.fa	ariba
ariba/tests/data/reference_data_load_input_check_seq_names.bad.csv.1	ariba
ariba/tests/data/reference_data_load_input_check_seq_names.bad.csv.2	ariba
ariba/tests/data/reference_data_load_input_check_seq_names.bad.fa.1	ariba
ariba/tests/data/reference_data_load_input_check_seq_names.bad.fa.2	ariba
ariba/tests/data/reference_data_load_input_check_seq_names.good.csv.1	ariba
ariba/tests/data/reference_data_load_input_check_seq_names.good.csv.2	ariba
ariba/tests/data/reference_data_load_input_check_seq_names.good.fa.1	ariba
ariba/tests/data/reference_data_load_input_check_seq_names.good.fa.2	ariba
ariba/tests/data/reference_data_load_metadata_tsv.tsv	ariba
ariba/tests/data/reference_data_load_rename_file.tsv	ariba
ariba/tests/data/reference_data_remove_bad_genes.in.fa	ariba
ariba/tests/data/reference_data_remove_bad_genes.in.tsv	ariba
ariba/tests/data/reference_data_rename_sequences.fa	ariba
ariba/tests/data/reference_data_rename_sequences_metadata.tsv	ariba
ariba/tests/data/reference_data_sequence.in.fa	ariba
ariba/tests/data/reference_data_sequence.in.tsv	ariba
ariba/tests/data/reference_data_sequence_type.in.fa	ariba
ariba/tests/data/reference_data_sequence_type.in.tsv	ariba
ariba/tests/data/reference_data_test_all_non_wild_type_variants.ref.fa	ariba
ariba/tests/data/reference_data_test_all_non_wild_type_variants.tsv	ariba
ariba/tests/data/reference_data_test_cluster_with_cdhit.expected.clusters.tsv	ariba
ariba/tests/data/reference_data_test_cluster_with_cdhit.in.fa	ariba
ariba/tests/data/reference_data_test_cluster_with_cdhit.in.tsv	ariba
ariba/tests/data/reference_data_test_remove_bad_genes.log	ariba
ariba/tests/data/reference_data_test_rename_sequences.out	ariba
ariba/tests/data/reference_data_test_write_cluster_allocation_file.expected	ariba
ariba/tests/data/reference_data_test_write_seqs_to_fasta.expected.fa	ariba
ariba/tests/data/reference_data_test_write_seqs_to_fasta.in.fa	ariba
ariba/tests/data/reference_data_test_write_seqs_to_fasta.in.tsv	ariba
ariba/tests/data/reference_data_write_metadata_tsv.expected.tsv	ariba
ariba/tests/data/reference_data_write_metadata_tsv.tsv	ariba
ariba/tests/data/reference_data_write_sequences_to_files.all.fa	ariba
ariba/tests/data/reference_data_write_sequences_to_files.gene.fa	ariba
ariba/tests/data/reference_data_write_sequences_to_files.gene.varonly.fa	ariba
ariba/tests/data/reference_data_write_sequences_to_files.noncoding.fa	ariba
ariba/tests/data/reference_data_write_sequences_to_files.noncoding.varonly.fa	ariba
ariba/tests/data/report_filter_test_init_bad.tsv	ariba
ariba/tests/data/report_filter_test_init_good.tsv	ariba
ariba/tests/data/report_filter_test_load_report_bad.tsv	ariba
ariba/tests/data/report_filter_test_load_report_good.tsv	ariba
ariba/tests/data/report_filter_test_run.expected.tsv	ariba
ariba/tests/data/report_filter_test_run.in.tsv	ariba
ariba/tests/data/report_filter_test_write_report.tsv	ariba
ariba/tests/data/report_flag_expander.run.in.tsv	ariba
ariba/tests/data/report_flag_expander.run.out.tsv	ariba
ariba/tests/data/samtools_variants_make_vcf_and_depths_files.asmbly.fa	ariba
ariba/tests/data/samtools_variants_make_vcf_and_depths_files.asmbly.fa.fai	ariba
ariba/tests/data/samtools_variants_make_vcf_and_depths_files.bam	ariba
ariba/tests/data/samtools_variants_make_vcf_and_depths_files.expect.cov	ariba
ariba/tests/data/samtools_variants_make_vcf_and_depths_files.expect.depths.gz	ariba
ariba/tests/data/samtools_variants_make_vcf_and_depths_files.expect.vcf	ariba
ariba/tests/data/samtools_variants_make_vcf_and_depths_files.for_reads.fa	ariba
ariba/tests/data/samtools_variants_make_vcf_and_depths_files.reads_1.fq	ariba
ariba/tests/data/samtools_variants_make_vcf_and_depths_files.reads_2.fq	ariba
ariba/tests/data/samtools_variants_test_get_depths_at_position.bam	ariba
ariba/tests/data/samtools_variants_test_get_depths_at_position.ref.fa	ariba
ariba/tests/data/samtools_variants_test_get_depths_at_position.ref.fa.fai	ariba
ariba/tests/data/samtools_variants_test_get_read_depths.gz	ariba
ariba/tests/data/samtools_variants_test_get_read_depths.gz.tbi	ariba
ariba/tests/data/samtools_variants_test_get_variant_positions_from_vcf.vcf	ariba
ariba/tests/data/samtools_variants_test_get_variants.read_depths.gz	ariba
ariba/tests/data/samtools_variants_test_get_variants.read_depths.gz.tbi	ariba
ariba/tests/data/samtools_variants_test_get_variants.vcf	ariba
ariba/tests/data/samtools_variants_test_total_depth_per_contig	ariba
ariba/tests/data/samtools_variants_test_variants_in_coords.vcf	ariba
ariba/tests/data/summary_gather_unfiltered_output_data.in.1.tsv	ariba
ariba/tests/data/summary_gather_unfiltered_output_data.in.2.tsv	ariba
ariba/tests/data/summary_sample_test_column_names_tuples_and_het_snps.tsv	ariba
ariba/tests/data/summary_sample_test_column_summary_data.tsv	ariba
ariba/tests/data/summary_sample_test_load_file.in.tsv	ariba
ariba/tests/data/summary_sample_test_non_synon_variants.tsv	ariba
ariba/tests/data/summary_sample_test_var_groups.tsv	ariba
ariba/tests/data/summary_test_init.fofn	ariba
ariba/tests/data/summary_test_load_fofn	ariba
ariba/tests/data/summary_test_load_input_files.1.tsv	ariba
ariba/tests/data/summary_test_load_input_files.2.tsv	ariba
ariba/tests/data/summary_test_newick_from_dist_matrix.distances	ariba
ariba/tests/data/summary_test_whole_run.in.1.tsv	ariba
ariba/tests/data/summary_test_whole_run.in.2.tsv	ariba
ariba/tests/data/summary_test_whole_run.out.csv	ariba
ariba/tests/data/summary_test_write_distance_matrix.distances	ariba
ariba/tests/data/summary_to_matrix.1.tsv	ariba
ariba/tests/data/summary_to_matrix.2.tsv	ariba
ariba/tests/data/test_common_cat_files.in.1	ariba
ariba/tests/data/test_common_cat_files.in.2	ariba
ariba/tests/data/test_common_cat_files.in.3	ariba
ariba/tests/data/test_common_cat_files.out	ariba
ariba/tests/data/vfdb_parser_test_run.in.fa	ariba
ariba/tests/data/vfdb_parser_test_run.out.fa	ariba
ariba/tests/data/vfdb_parser_test_run.out.tsv	ariba
ariba/tests/external_progs_test.py	ariba
ariba/tests/faidx_test.py	ariba
ariba/tests/flag_test.py	ariba
ariba/tests/histogram_test.py	ariba
ariba/tests/link_test.py	ariba
ariba/tests/mapping_test.py	ariba
ariba/tests/megares_data_finder_test.py	ariba
ariba/tests/megares_zip_parser_test.py	ariba
ariba/tests/mic_plotter_test.py	ariba
ariba/tests/mlst_profile_test.py	ariba
ariba/tests/mlst_reporter_test.py	ariba
ariba/tests/pubmlst_getter_test.py	ariba
ariba/tests/pubmlst_ref_preparer_test.py	ariba
ariba/tests/read_filter_test.py	ariba
ariba/tests/read_store_test.py	ariba
ariba/tests/ref_preparer_test.py	ariba
ariba/tests/ref_seq_chooser_test.py	ariba
ariba/tests/reference_data_test.py	ariba
ariba/tests/report_filter_test.py	ariba
ariba/tests/report_flag_expander_test.py	ariba
ariba/tests/samtools_variants_test.py	ariba
ariba/tests/scaffold_graph_test.py	ariba
ariba/tests/sequence_metadata_test.py	ariba
ariba/tests/sequence_variant_test.py	ariba
ariba/tests/summary_cluster_test.py	ariba
ariba/tests/summary_cluster_variant_test.py	ariba
ariba/tests/summary_sample_test.py	ariba
ariba/tests/summary_test.py	ariba
ariba/tests/test_refdata_query.py	ariba
ariba/tests/versions_test.py	ariba
ariba/tests/vfdb_parser_test.py	ariba
ariba/versions.py	ariba
ariba/vfdb_parser.py	ariba
.
15273c
aclocal.m4	cockpit,erlang-p1-iconv,gajim,spl-linux
acpi_call.c	acpi-call
.
426c
README.md	acpi-call,ariba,boinc,calendar-exchange-provider,cockpit,erlang-jiffy,erlang-meck,erlang-p1-cache-tab,erlang-p1-iconv,erlang-p1-mysql,erlang-p1-oauth2,erlang-p1-pam,erlang-p1-pgsql,erlang-p1-sip,erlang-p1-stringprep,erlang-p1-stun,erlang-p1-tls,erlang-p1-utils,erlang-p1-xml,erlang-p1-xmpp,erlang-p1-yaml,erlang-p1-zlib,fermi-lite,gajim-antispam,golang-github-klauspost-reedsolomon,golang-github-xtaci-kcp,golang-github-xtaci-smux,kcptun,minimap,open-vm-tools,python-pymummer,roary,shadowsocks-libev,simple-obfs
.
424c
README	cd-hit,gajim,gramps,haproxy,lava-dispatcher,lava-server,libbloom,spades,tlp
.
422a
NOTICE	erlang-meck
.
420a
Makefile.mix	erlang-p1-xml
.
419c
Makefile.in	cockpit,gajim,mash,spl-linux
.
417c
Makefile	acpi-call,cd-hit,erlang-jiffy,erlang-p1-cache-tab,erlang-p1-iconv,erlang-p1-mysql,erlang-p1-oauth2,erlang-p1-pam,erlang-p1-pgsql,erlang-p1-sip,erlang-p1-stringprep,erlang-p1-stun,erlang-p1-tls,erlang-p1-utils,erlang-p1-xml,erlang-p1-xmpp,erlang-p1-yaml,erlang-p1-zlib,fermi-lite,haproxy,libbloom,minimap,tlp
.
415c
MANIFEST.in	ariba,gramps,lava-dispatcher,lava-server
.
413a
LICENSE.txt	erlang-p1-cache-tab,erlang-p1-iconv,erlang-p1-pam,erlang-p1-sip,erlang-p1-stringprep,erlang-p1-stun,erlang-p1-tls,erlang-p1-utils,erlang-p1-xml,erlang-p1-xmpp,erlang-p1-yaml,erlang-p1-zlib,fermi-lite,mash,minimap
.
412c
INSTALL.txt	mash
LICENSE	ariba,erlang-jiffy,erlang-meck,erlang-p1-oauth2,golang-github-klauspost-reedsolomon,golang-github-xtaci-kcp,golang-github-xtaci-smux,gramps,haproxy,igtf-policy-bundle,libbloom,libsodium,python-pymummer,shadowsocks-libev,simple-obfs,spades,tlp
LICENSE.ALL	erlang-p1-stringprep
LICENSE.TCL	erlang-p1-stringprep
.
406a
FET.pl	cd-hit
.
405a
EPLICENSE	erlang-p1-pgsql
.
215c
Dockerfile	ariba,kcptun,roary
.
212c
ChangeLog	cd-hit,gajim,gramps,libsodium
.
207c
CONTRIBUTING.md	erlang-meck
COPYING	boinc,cockpit,erlang-p1-mysql,gajim,gramps,lava-dispatcher,shadowsocks-libev,simple-obfs,spl-linux,tlp
.
205a
CODE_OF_CONDUCT.md	erlang-meck
.
203c
CHANGELOG.md	calendar-exchange-provider,erlang-meck,erlang-p1-cache-tab,erlang-p1-iconv,erlang-p1-mysql,erlang-p1-oauth2,erlang-p1-pam,erlang-p1-pgsql,erlang-p1-sip,erlang-p1-stringprep,erlang-p1-stun,erlang-p1-tls,erlang-p1-utils,erlang-p1-xml,erlang-p1-xmpp,erlang-p1-yaml,erlang-p1-zlib
.
201c
AUTHORS	ariba,cockpit,gajim,gramps,libsodium,python-pymummer,roary,shadowsocks-libev,simple-obfs,spl-linux,tlp
.
194c
.travis.yml	ariba,boinc,erlang-jiffy,erlang-meck,erlang-p1-cache-tab,erlang-p1-iconv,erlang-p1-mysql,erlang-p1-oauth2,erlang-p1-pgsql,erlang-p1-sip,erlang-p1-stringprep,erlang-p1-stun,erlang-p1-tls,erlang-p1-utils,erlang-p1-xml,erlang-p1-yaml,erlang-p1-zlib,golang-github-klauspost-reedsolomon,golang-github-xtaci-kcp,golang-github-xtaci-smux,gramps,kcptun,libsodium,python-pymummer,roary
.
190a
.pc/use_bwa_compatible_fermi-lite.patch/ariba/ext/fml-asm_ariba.cpp	ariba
.pc/use_debian_mathjax.patch/doc/sphinx/conf.py	mash
.pc/use_debian_packaged_libs_for_extension.patch/setup.py	ariba
.scripts/meck-publish.sh	erlang-meck
.
149a
.pc/rename_bseq1_t.patch/README.md	fermi-lite
.pc/rename_bseq1_t.patch/bfc.c	fermi-lite
.pc/rename_bseq1_t.patch/bseq.c	fermi-lite
.pc/rename_bseq1_t.patch/example.c	fermi-lite
.pc/rename_bseq1_t.patch/fml.h	fermi-lite
.pc/rename_bseq1_t.patch/internal.h	fermi-lite
.pc/rename_bseq1_t.patch/misc.c	fermi-lite
.
148a
.pc/rebar.test.config.patch/rebar.test.config	erlang-p1-oauth2
.pc/remove-deps.diff/rebar.config	erlang-p1-cache-tab,erlang-p1-iconv,erlang-p1-sip,erlang-p1-stringprep,erlang-p1-stun,erlang-p1-tls,erlang-p1-xml,erlang-p1-xmpp,erlang-p1-yaml
.pc/remove_git_clean/Makefile	erlang-jiffy
.
144a
.pc/parallel.patch/Makefile.in	mash
.
141a
.pc/make_shared_lib/Makefile	fermi-lite,minimap
.pc/mips-atomic.diff/c_src/ets_cache.c	erlang-p1-cache-tab
.pc/mips-atomic.diff/rebar.config	erlang-p1-cache-tab
.
140a
.pc/link_dynamically_against_capnp.patch/Makefile.in	mash
.
139a
.pc/hardening.patch/Makefile.in	mash
.pc/hardening/Makefile	fermi-lite,minimap
.
125a
.pc/fix_makefile/Makefile	erlang-jiffy
.
121a
.pc/fix-includes.diff/include/xmpp.hrl	erlang-p1-xmpp
.pc/fix-includes.diff/src/esip_socket.erl	erlang-p1-sip
.
98a
.pc/drop_memcpy_wrapper.patch/Makefile.in	mash
.pc/enable_help2man.patch/cd-hit-2d-para.pl	cd-hit
.pc/enable_help2man.patch/cd-hit-div.pl	cd-hit
.pc/enable_help2man.patch/cd-hit-para.pl	cd-hit
.pc/ensure_64bit_value/kdq.h	minimap
.pc/epam_bin_path.diff/src/epam.erl	erlang-p1-pam
.pc/f9de643f167cfa274862d323694c1bf5b57d3be2.patch/src/fast_tls.erl	erlang-p1-tls
.
71a
.pc/bcf_seqlib.patch/bfc.c	fermi-lite
.pc/bcf_seqlib.patch/bfc.h	fermi-lite
.
53c
.pc/applied-patches	acpi-call,ariba,boinc,calendar-exchange-provider,cd-hit,cockpit,erlang-jiffy,erlang-meck,erlang-p1-cache-tab,erlang-p1-iconv,erlang-p1-mysql,erlang-p1-oauth2,erlang-p1-pam,erlang-p1-pgsql,erlang-p1-sip,erlang-p1-stringprep,erlang-p1-stun,erlang-p1-tls,erlang-p1-utils,erlang-p1-xml,erlang-p1-xmpp,erlang-p1-yaml,erlang-p1-zlib,fermi-lite,gajim,gajim-antispam,golang-github-klauspost-reedsolomon,golang-github-xtaci-kcp,golang-github-xtaci-smux,gramps,haproxy,igtf-policy-bundle,kcptun,lava-dispatcher,lava-server,libbloom,libsodium,mash,minimap,open-vm-tools,python-pymummer,roary,shadowsocks-libev,simple-obfs,spades,spl-linux,tlp,webkit2gtk
.pc/b87766daf8df5e84463223df538fe3c82bc89def.patch/c_src/fast_tls.c	erlang-p1-tls
.
50a
.pc/a4e6a8f6a66836f62471f7fb6df3cc590689fdfa.patch/rebar.config	erlang-p1-sip
.pc/a4e6a8f6a66836f62471f7fb6df3cc590689fdfa.patch/rebar.config.script	erlang-p1-sip
.pc/a4e6a8f6a66836f62471f7fb6df3cc590689fdfa.patch/src/esip.erl	erlang-p1-sip
.pc/a4e6a8f6a66836f62471f7fb6df3cc590689fdfa.patch/src/esip_client_transaction.erl	erlang-p1-sip
.pc/a4e6a8f6a66836f62471f7fb6df3cc590689fdfa.patch/src/esip_server_transaction.erl	erlang-p1-sip
.
16a
.pc/0002-Fix-build-4.12-copy-from-user.patch/acpi_call.c	acpi-call
.
12a
.pc/0001-Fix-compatibility-with-Linux-3.17.patch/acpi_call.c	acpi-call
.
8,10c
.pc/.quilt_patches	acpi-call,ariba,boinc,calendar-exchange-provider,cd-hit,cockpit,erlang-jiffy,erlang-meck,erlang-p1-cache-tab,erlang-p1-iconv,erlang-p1-mysql,erlang-p1-oauth2,erlang-p1-pam,erlang-p1-pgsql,erlang-p1-sip,erlang-p1-stringprep,erlang-p1-stun,erlang-p1-tls,erlang-p1-utils,erlang-p1-xml,erlang-p1-xmpp,erlang-p1-yaml,erlang-p1-zlib,fermi-lite,gajim,gajim-antispam,golang-github-klauspost-reedsolomon,golang-github-xtaci-kcp,golang-github-xtaci-smux,gramps,haproxy,igtf-policy-bundle,kcptun,lava-dispatcher,lava-server,libbloom,libsodium,mash,minimap,open-vm-tools,python-pymummer,roary,shadowsocks-libev,simple-obfs,spades,spl-linux,tlp,webkit2gtk
.pc/.quilt_series	acpi-call,ariba,boinc,calendar-exchange-provider,cd-hit,cockpit,erlang-jiffy,erlang-meck,erlang-p1-cache-tab,erlang-p1-iconv,erlang-p1-mysql,erlang-p1-oauth2,erlang-p1-pam,erlang-p1-pgsql,erlang-p1-sip,erlang-p1-stringprep,erlang-p1-stun,erlang-p1-tls,erlang-p1-utils,erlang-p1-xml,erlang-p1-xmpp,erlang-p1-yaml,erlang-p1-zlib,fermi-lite,gajim,gajim-antispam,golang-github-klauspost-reedsolomon,golang-github-xtaci-kcp,golang-github-xtaci-smux,gramps,haproxy,igtf-policy-bundle,kcptun,lava-dispatcher,lava-server,libbloom,libsodium,mash,minimap,open-vm-tools,python-pymummer,roary,shadowsocks-libev,simple-obfs,spades,spl-linux,tlp,webkit2gtk
.pc/.version	acpi-call,ariba,boinc,calendar-exchange-provider,cd-hit,cockpit,erlang-jiffy,erlang-meck,erlang-p1-cache-tab,erlang-p1-iconv,erlang-p1-mysql,erlang-p1-oauth2,erlang-p1-pam,erlang-p1-pgsql,erlang-p1-sip,erlang-p1-stringprep,erlang-p1-stun,erlang-p1-tls,erlang-p1-utils,erlang-p1-xml,erlang-p1-xmpp,erlang-p1-yaml,erlang-p1-zlib,fermi-lite,gajim,gajim-antispam,golang-github-klauspost-reedsolomon,golang-github-xtaci-kcp,golang-github-xtaci-smux,gramps,haproxy,igtf-policy-bundle,kcptun,lava-dispatcher,lava-server,libbloom,libsodium,mash,minimap,open-vm-tools,python-pymummer,roary,shadowsocks-libev,simple-obfs,spades,spl-linux,tlp,webkit2gtk
.
4,5c
.github/ISSUE_TEMPLATE.md	erlang-meck,tlp
.github_changelog_generator	erlang-meck
.gitignore	ariba,boinc,erlang-jiffy,erlang-meck,fermi-lite,golang-github-klauspost-reedsolomon,golang-github-xtaci-kcp,golang-github-xtaci-smux,gramps,haproxy,kcptun,lava-dispatcher,lava-server,libbloom,libsodium,minimap,python-pymummer,roary,simple-obfs
.
