{"push_id":902019770,"size":19,"distinct_size":1,"ref":"refs/heads/feature/compression_threads","head":"6737c5c8074943b51e18fd53458f41a30d623fb7","before":"284099c758013ed0e2996b9e92e846d6bdfc580c","commits":[{"sha":"983067a2646d82baeb4f869e8014f6ca63fd477e","author":{"email":"b48e0e91d6a7b0f03328f39c48db102a17c97190@sanger.ac.uk","name":"Petr Danecek"},"message":"cnv: New -k option, fixed non-functional parsing of -dfloat,float","distinct":false,"url":"https://api.github.com/repos/samtools/bcftools/commits/983067a2646d82baeb4f869e8014f6ca63fd477e"},{"sha":"2fc54de889a241372f26ff41ee7b58989484ab6f","author":{"email":"b48e0e91d6a7b0f03328f39c48db102a17c97190@sanger.ac.uk","name":"Petr Danecek"},"message":"CNV output include number of sites/hets in regions","distinct":false,"url":"https://api.github.com/repos/samtools/bcftools/commits/2fc54de889a241372f26ff41ee7b58989484ab6f"},{"sha":"e325cd0e46d3219bf556e0392c83bde8e7ffa1ef","author":{"email":"b48e0e91d6a7b0f03328f39c48db102a17c97190@sanger.ac.uk","name":"Petr Danecek"},"message":"Reduce memory consumption in cnv plotting script","distinct":false,"url":"https://api.github.com/repos/samtools/bcftools/commits/e325cd0e46d3219bf556e0392c83bde8e7ffa1ef"},{"sha":"3c4ddc79d6c8c5d99d5ef02c8d6d747692ef7fe9","author":{"email":"b48e0e91d6a7b0f03328f39c48db102a17c97190@sanger.ac.uk","name":"Petr Danecek"},"message":"Added cnv and polysomy commands to the docs","distinct":false,"url":"https://api.github.com/repos/samtools/bcftools/commits/3c4ddc79d6c8c5d99d5ef02c8d6d747692ef7fe9"},{"sha":"2e5fda73099ea237db5d2c0b98881509a1e81ab7","author":{"email":"4081f471c57da10c91f8e26ca2a349938ce26dd5@sanger.ac.uk","name":"John Marshall"},"message":"Dynamically export bcftools symbols to plugins\n\n...instead of linking the plugins against libhts.so.  This simplifies\nbuilding and installation, as plugins no longer need to be able to find\nlibhts.so/.dylib at runtime -- which to date has unfortunately often\nbeen done via $LD_LIBRARY_PATH.\n\nOn OS X, build plugins as Mach-O bundles rather than shared libraries\n(and ensure that bcftools is built first, so is available for use with\n-bundle_loader).  Fixes #225.\n\n(TODO) The advice in print_plugin_usage_hint() should be revisited.\n\nWhen bcftools is linked to libhts.a statically, there is a small chance\nthat a plugin will need HTSlib functions that have not been pulled in by\nthe bcftools executable.  This is surely unlikely, and can be prevented\nby linking bcftools or your plugin against a shared libhts.so.\n\nFixes #249; fixes #224; supersedes and closes #254.","distinct":false,"url":"https://api.github.com/repos/samtools/bcftools/commits/2e5fda73099ea237db5d2c0b98881509a1e81ab7"},{"sha":"db3d87d21c16cada798daaf4bd8aea5e83e830c8","author":{"email":"4081f471c57da10c91f8e26ca2a349938ce26dd5@sanger.ac.uk","name":"John Marshall"},"message":"Fix error message segfault [minor]","distinct":false,"url":"https://api.github.com/repos/samtools/bcftools/commits/db3d87d21c16cada798daaf4bd8aea5e83e830c8"},{"sha":"63cffa41eae7b0349b56a44e400fe2f963e69ca2","author":{"email":"b48e0e91d6a7b0f03328f39c48db102a17c97190@sanger.ac.uk","name":"Petr Danecek"},"message":"further fixes in vcf2sex\n\n- check the return status of bcf_get_fmt to prevent segfaults when GT tag is\n  not present\n- fix a silly error in assigning homs and hets from likelihoods\n- set to missing when most het and hom equally likely\n\nCloses #347","distinct":false,"url":"https://api.github.com/repos/samtools/bcftools/commits/63cffa41eae7b0349b56a44e400fe2f963e69ca2"},{"sha":"3eb86dca612545d97a190d412d2e3673ff0f6212","author":{"email":"0c7948b6e77e16a7c2f08e676c85de2b1aa6fa69@hhu.de","name":"David Laehnemann"},"message":"plot-vcfstats: plotting of sample names fixed\n\nPlotting of sample names instead of sample ID numbers (flags -s/--sample-names) in plot-vcfstats did not work as the first input to plt.xticks in <prefix>-plot.py was an array of strings instead of an array of integers for all by-sample plots. A simple call of int() around the row[0] argument in the list comprehension fixes that.","distinct":false,"url":"https://api.github.com/repos/samtools/bcftools/commits/3eb86dca612545d97a190d412d2e3673ff0f6212"},{"sha":"6470ba4bdc8decc2d80f8ff42f40dd68cfa41c5d","author":{"email":"a659913de03567a1dba11ecf43602c3d5ffd1688@sanger.ac.uk","name":"Shane McCarthy"},"message":"Merge pull request #352 from dlaehnemann/develop\n\nplot-vcfstats: plotting of sample names fixed","distinct":false,"url":"https://api.github.com/repos/samtools/bcftools/commits/6470ba4bdc8decc2d80f8ff42f40dd68cfa41c5d"},{"sha":"6710191a0cba3327d8aa63d1e6dfc08c748c4203","author":{"email":"a659913de03567a1dba11ecf43602c3d5ffd1688@sanger.ac.uk","name":"Shane McCarthy"},"message":"Merge branch 'feature/cnv' into develop","distinct":false,"url":"https://api.github.com/repos/samtools/bcftools/commits/6710191a0cba3327d8aa63d1e6dfc08c748c4203"},{"sha":"459a7ab1ca94dff1d3fda324c2c657b181c214c7","author":{"email":"a659913de03567a1dba11ecf43602c3d5ffd1688@sanger.ac.uk","name":"Shane McCarthy"},"message":"update docs from asciidoc","distinct":false,"url":"https://api.github.com/repos/samtools/bcftools/commits/459a7ab1ca94dff1d3fda324c2c657b181c214c7"},{"sha":"37b0ddc34ba17fbf58bdb96a19f4af14e7d158c5","author":{"email":"a659913de03567a1dba11ecf43602c3d5ffd1688@sanger.ac.uk","name":"Shane McCarthy"},"message":"add *.dSYM to .gitignore\n\nThese files are generated on Mac OS X after 2e5fda73099ea237db5d2c0b98881509a1e81ab7","distinct":false,"url":"https://api.github.com/repos/samtools/bcftools/commits/37b0ddc34ba17fbf58bdb96a19f4af14e7d158c5"},{"sha":"8e8679d28a2bde33cc3a67c7afbde10b81f0b8c1","author":{"email":"b48e0e91d6a7b0f03328f39c48db102a17c97190@sanger.ac.uk","name":"Petr Danecek"},"message":"Prevent empty PL fields on BCF output with \"call -C alleles\"","distinct":false,"url":"https://api.github.com/repos/samtools/bcftools/commits/8e8679d28a2bde33cc3a67c7afbde10b81f0b8c1"},{"sha":"03c60cfd3c3ad5715f3795faa1101d58281a2d86","author":{"email":"a659913de03567a1dba11ecf43602c3d5ffd1688@sanger.ac.uk","name":"Shane McCarthy"},"message":"add POS as a filter column","distinct":false,"url":"https://api.github.com/repos/samtools/bcftools/commits/03c60cfd3c3ad5715f3795faa1101d58281a2d86"},{"sha":"1a55e45051eb5896e719f62d13992eebb8c64a7f","author":{"email":"a659913de03567a1dba11ecf43602c3d5ffd1688@sanger.ac.uk","name":"Shane McCarthy"},"message":"Merge pull request #354 from samtools/feature/filter_pos\n\nadd POS as a filter column","distinct":false,"url":"https://api.github.com/repos/samtools/bcftools/commits/1a55e45051eb5896e719f62d13992eebb8c64a7f"},{"sha":"3aa989e2191f68441f6be8d07d99d3160442f65a","author":{"email":"b48e0e91d6a7b0f03328f39c48db102a17c97190@sanger.ac.uk","name":"Petr Danecek"},"message":"Fix typo: annotate -x ^FORMAT/TAG did not work","distinct":false,"url":"https://api.github.com/repos/samtools/bcftools/commits/3aa989e2191f68441f6be8d07d99d3160442f65a"},{"sha":"5d90843e0b271233a42fbf2579c4daa324f4dd30","author":{"email":"a659913de03567a1dba11ecf43602c3d5ffd1688@sanger.ac.uk","name":"mcshane"},"message":"split out test input files for -c and -m calling\n\nthis is to allow pulling in the bugfix from pd3/bcftools@47ab239744ab2aaf2165d1542010ba7e6ba7dafd\nthe `-c' calling mode is not ready for PLs with missing values\netc yet that are added to the test files in that commit.","distinct":false,"url":"https://api.github.com/repos/samtools/bcftools/commits/5d90843e0b271233a42fbf2579c4daa324f4dd30"},{"sha":"71921ca39706fb7b15165ed76729c24a6b89e8cf","author":{"email":"b48e0e91d6a7b0f03328f39c48db102a17c97190@sanger.ac.uk","name":"Petr Danecek"},"message":"call -mC alleles fix: Do not take X as last in ALT list for granted","distinct":false,"url":"https://api.github.com/repos/samtools/bcftools/commits/71921ca39706fb7b15165ed76729c24a6b89e8cf"},{"sha":"6737c5c8074943b51e18fd53458f41a30d623fb7","author":{"email":"a659913de03567a1dba11ecf43602c3d5ffd1688@sanger.ac.uk","name":"Shane McCarthy"},"message":"add --threads option for output compression threads\n\n* `--threads` option added to commands that output VCF/BCF\n* add this new option to the docs","distinct":true,"url":"https://api.github.com/repos/samtools/bcftools/commits/6737c5c8074943b51e18fd53458f41a30d623fb7"}]}