{"shas":[["aa23a89b727c02be1f29f03a9d43c207257d8be1","94ddc6985b47aef772521e302594241f46a8f665@biotech.uni-tuebingen.de","Fix File::Path calls for older File::Path versions","Kai Blin"],["d5faf5eddbc4c517cca10e544a1d099e6936b12e","edb815ca89c31e501cb0f48d4b85f75a7b28f923@bioperl.org","add primary_id as a constructor parameter","Chris Fields"],["6fae6bd18f12ff9c34ceaa1d9fb7564b08f78b56","68c46a606457643eab92053c1c05574abb26f861@bioperl.org","Merge remote branch 'upstream/master'","jason"],["c303368feaf4f2815d70ecd75e080526f490b233","edb815ca89c31e501cb0f48d4b85f75a7b28f923@bioperl.org","add check for undef in array of IDs","Chris Fields"],["ff86499dd10464ea6498305f65a05aeb392f6676","9971cf12989856c99cc94b3027a64a32103884a8@novozymes.com","Test that long label qualifiers can be parsed.","Adam Sjøgren"],["fd85538e8904f84fa3095bb4aa2ae79a9e34f0a2","9971cf12989856c99cc94b3027a64a32103884a8@novozymes.com","Quote qualifiers that are so long that they are line wrapped.","Adam Sjøgren"],["d361d400501069cb0a8ed7a8926e2c096223da66","edb815ca89c31e501cb0f48d4b85f75a7b28f923@bioperl.org","remove IO::String dependency","Chris Fields"],["4bf96c90cbb4f1bd13a3f4a443c3188e16e2556d","68c46a606457643eab92053c1c05574abb26f861@bioperl.org","Merge remote branch 'upstream/master'","jason"],["322ac7fa0d887311a8458157eaccde0a1e914e2a","79e2475f81a6317276bf7cbb3958b20d289b78df@ebi-002.ebi.ac.uk","Rewrite the TreeIO nhx and newick parser and add a bunch of round-trip tests.","Greg Jordan"],["2eca6fcfbde3c8639941805670e93a68baef1c97","93149ebdfe6c5022f3f862634bef2eec85065f75@virginia.edu","updated FASTA result parsing for version 3.6; FASTA hits may now include more than one HSP, and report E2() expectations via \\$hsp->evalue2()","Aaron J. Mackey"],["0ae94bafb9ec919a477ecc5b20024ec9482afbe4","5358d8153259ae997db8b691037249f0bf28e4b7@cornell.edu","added tests for obo.pm parsing secondary ids","Naama Menda"],["6285ff0f21df957cb702fd210daa06454390f56a","edb815ca89c31e501cb0f48d4b85f75a7b28f923@bioperl.org","update manifest","Chris Fields"],["f4a2731cb2e9d83f1c317cea2acf598db676ecc4","edb815ca89c31e501cb0f48d4b85f75a7b28f923@bioperl.org","update MANIFEST.SKIP","Chris Fields"],["fb5c8bb0f5d3e2367e52bc37f638ec21f69667bf","3692bfa45759a67d83aedf0045f6cb635a966abf@leto.net","Merge branch 'master' of http://github.com/nmenda/bioperl-live into nmenda-master","Jonathan \"Duke\" Leto"],["52b69943dc5fb8d9eafbd38748776e42a63ec366","3692bfa45759a67d83aedf0045f6cb635a966abf@leto.net","Add note to Changes about new OBO parsing features","Jonathan \"Duke\" Leto"],["18b0fd2233cc6a7b359b1ab7a6902159e373b7f4","2dbc2fd2358e1ea1b7a6bc08ea647b9a337ac92d@davemessina.com","typo in docs","Dave Messina"],["263f5d700735de9dbef998e86263fe8f68dd88b8","68c46a606457643eab92053c1c05574abb26f861@bioperl.org","Merge remote branch 'upstream/master'","jason"],["5d928aee0d2a8963939615d4fedeedb867769425","94ddc6985b47aef772521e302594241f46a8f665@biotech.uni-tuebingen.de","Bio::SearchIO::hmmer3: Fix the hmm and query start/stop positions\n\nWhile writing the tests I misunderstood the values in the hmmer output. Fixed the tests to test for the correct values, fixed the parser to report the correct values.","Kai Blin"],["002d1e64e69437ea20b022ac42c2c8a27c49ba29","94ddc6985b47aef772521e302594241f46a8f665@biotech.uni-tuebingen.de","SearchIO::hmmer3: Correctly parse out aligments\n\nThe hmmer3 parser failed to correctly parse out the hit sequence, the\nconservation sequence and the query sequence from alignments.\n\nFixed bug #3136","Kai Blin"],["7a0b8512bfc07203de13fd810224ef017dd5c814","94ddc6985b47aef772521e302594241f46a8f665@biotech.uni-tuebingen.de","Bio::SearchIO::hmmer3: Deal with possible model track\n\nSome hmmer3 result files have a line giving a secondary structure model.\nDeal with these results while not breaking the existing files.","Kai Blin"]],"ref":"refs/heads/master","size":411,"head":"ac239cba88e992ad4cbfe4ab3571a4294452f1b1","push_id":37655514}