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Title: Commits · SelfHacked/bcftools · GitHub

Open Graph Title: Commits · SelfHacked/bcftools

X Title: Commits · SelfHacked/bcftools

Description: This is the official development repository for BCFtools. To compile, the develop branch of htslib is needed: git clone --branch=develop git://github.com/samtools/htslib.git htslib - Commits · SelfHacked/bcftools

Open Graph Description: This is the official development repository for BCFtools. To compile, the develop branch of htslib is needed: git clone --branch=develop git://github.com/samtools/htslib.git htslib - Commits · Self...

X Description: This is the official development repository for BCFtools. To compile, the develop branch of htslib is needed: git clone --branch=develop git://github.com/samtools/htslib.git htslib - Commits · Self...

Opengraph URL: https://github.com/SelfHacked/bcftools

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Domain: patch-diff.githubusercontent.com

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Rename trio-dnm to trio-dnm2 to avoid confusionhttps://patch-diff.githubusercontent.com/SelfHacked/bcftools/commit/8a744dd8591946f6ae013fe8d18b6f7101f06da3
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Merge pull request #1356 from CreRecombinase/patch-1https://patch-diff.githubusercontent.com/SelfHacked/bcftools/commit/6b3df6493b44117a43947f1d0f16c922bb158c2e
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Merge pull request #1355 from jmarshall/merge_fmt_strhttps://patch-diff.githubusercontent.com/SelfHacked/bcftools/commit/29c48ebe99a37b228c37da616a18d82fb03d9e9a
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Merge pull request #1351 from jmarshall/mischttps://patch-diff.githubusercontent.com/SelfHacked/bcftools/commit/f599cfc989949cdd8cd415abb6f4f28ce0d9a7b5
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https://patch-diff.githubusercontent.com/SelfHacked/bcftools/tree/f599cfc989949cdd8cd415abb6f4f28ce0d9a7b5
[NEWS] Revamp of `bcftools call -G`https://patch-diff.githubusercontent.com/SelfHacked/bcftools/commit/0f4aed2936fdfc9df7f81e94ea8f22071acf236d
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https://patch-diff.githubusercontent.com/SelfHacked/bcftools/tree/0f4aed2936fdfc9df7f81e94ea8f22071acf236d
remove error before switch when fmt->type!=int8_thttps://patch-diff.githubusercontent.com/SelfHacked/bcftools/commit/1fdc54162a99b3e433f633788042124a102a9db8
1fdc541https://patch-diff.githubusercontent.com/SelfHacked/bcftools/commit/1fdc54162a99b3e433f633788042124a102a9db8
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merge_format_string: Enlarge array for BCF_VL_A/BCF_VL_R toohttps://patch-diff.githubusercontent.com/SelfHacked/bcftools/commit/ff5dc521d91420e797aa745a8177763be13692b3
https://patch-diff.githubusercontent.com/jmarshall
jmarshallhttps://patch-diff.githubusercontent.com/SelfHacked/bcftools/commits?author=jmarshall
ff5dc52https://patch-diff.githubusercontent.com/SelfHacked/bcftools/commit/ff5dc521d91420e797aa745a8177763be13692b3
https://patch-diff.githubusercontent.com/SelfHacked/bcftools/tree/ff5dc521d91420e797aa745a8177763be13692b3
[NEWS] Major revamp of `bcftools +trio-dnm`https://patch-diff.githubusercontent.com/SelfHacked/bcftools/commit/07c4308f4bdea2f40d7691ba79f37601efe89ce9
https://patch-diff.githubusercontent.com/pd3
pd3https://patch-diff.githubusercontent.com/SelfHacked/bcftools/commits?author=pd3
07c4308https://patch-diff.githubusercontent.com/SelfHacked/bcftools/commit/07c4308f4bdea2f40d7691ba79f37601efe89ce9
https://patch-diff.githubusercontent.com/SelfHacked/bcftools/tree/07c4308f4bdea2f40d7691ba79f37601efe89ce9
Add new optional tag by `mpileup -a FORMAT/QS`https://patch-diff.githubusercontent.com/SelfHacked/bcftools/commit/9718479aca7b7250141778c6ad13a20029e19a45
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pd3https://patch-diff.githubusercontent.com/SelfHacked/bcftools/commits?author=pd3
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https://patch-diff.githubusercontent.com/SelfHacked/bcftools/tree/9718479aca7b7250141778c6ad13a20029e19a45
Changes to QUAL and ts/tv plotting statshttps://patch-diff.githubusercontent.com/SelfHacked/bcftools/commit/09f2dbdaf1462ba9f6814d6a8ce1223930a21282
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Add missing gtcheck testshttps://patch-diff.githubusercontent.com/SelfHacked/bcftools/commit/dc1182b5987312c35c364bc3627647f2e71f1dfa
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Include directly where neededhttps://patch-diff.githubusercontent.com/SelfHacked/bcftools/commit/3200bffffe30e61f6085130aa732bc7cb6f86c6f
https://patch-diff.githubusercontent.com/jmarshall
jmarshallhttps://patch-diff.githubusercontent.com/SelfHacked/bcftools/commits?author=jmarshall
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Remove generated test/*.fa.fai fileshttps://patch-diff.githubusercontent.com/SelfHacked/bcftools/commit/c22939f6ea5b1035a9f5cb76cde42dd7158b2932
https://patch-diff.githubusercontent.com/jmarshall
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https://patch-diff.githubusercontent.com/SelfHacked/bcftools/tree/c22939f6ea5b1035a9f5cb76cde42dd7158b2932
Various user-visible typo fixeshttps://patch-diff.githubusercontent.com/SelfHacked/bcftools/commit/77bd35da169fb1809cded3c031f143f0e6069d87
https://patch-diff.githubusercontent.com/jmarshall
jmarshallhttps://patch-diff.githubusercontent.com/SelfHacked/bcftools/commits?author=jmarshall
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Prevent internal dropping of samples on VCF input and VCF/BCF outputhttps://patch-diff.githubusercontent.com/SelfHacked/bcftools/commit/0987715cd8700a9db398166ce055783054e8d193
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More informative error message. Resolves #1128https://patch-diff.githubusercontent.com/SelfHacked/bcftools/commit/929d9ad6291354cb96ea9d5c63b5636e7858f3bc
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Add new `annotate --rename-annots` option to help fix broken VCFs. Resolves #1335https://patch-diff.githubusercontent.com/SelfHacked/bcftools/commit/ec5eb612ed020bc5d1ae98dcc487ba306259e0b6
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Make an assumption about start when strlen(REF)!=1. Resolves #1319https://patch-diff.githubusercontent.com/SelfHacked/bcftools/commit/a923acc5ad212926bac38b2c57517dba816a653f
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pd3https://patch-diff.githubusercontent.com/SelfHacked/bcftools/commits?author=pd3
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Do not phase genotypes that are not phased with `concat -l`. Fixes #1346https://patch-diff.githubusercontent.com/SelfHacked/bcftools/commit/c454e5fcfc0700397f285464b8653e0ec0e50137
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Merge branch 'develop' of github.com:samtools/bcftools into develophttps://patch-diff.githubusercontent.com/SelfHacked/bcftools/commit/9f2fa9f52da8818fc6de5c488acb82c808574a78
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Make F_MISSING work for sites with many ALT alleles. Fixes #1343https://patch-diff.githubusercontent.com/SelfHacked/bcftools/commit/3dd8b82584be49432edeeebe3a97dc3de8036e78
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Clarify how --n-matches works, allow to choose all sampleshttps://patch-diff.githubusercontent.com/SelfHacked/bcftools/commit/eec09685edb6baf98e5c2011e4c6cfb0cec3e298
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Merge pull request #1338 from jkbonfield/cirrus-cihttps://patch-diff.githubusercontent.com/SelfHacked/bcftools/commit/78003de6dc5f24257a33230040061b464a442d2b
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Update .travis/clone to match Samtools.https://patch-diff.githubusercontent.com/SelfHacked/bcftools/commit/761021b4ebe30c3480bcf0dea0e5103b948d513d
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jkbonfieldhttps://patch-diff.githubusercontent.com/SelfHacked/bcftools/commits?author=jkbonfield
761021bhttps://patch-diff.githubusercontent.com/SelfHacked/bcftools/commit/761021b4ebe30c3480bcf0dea0e5103b948d513d
https://patch-diff.githubusercontent.com/SelfHacked/bcftools/tree/761021b4ebe30c3480bcf0dea0e5103b948d513d
Add Cirrus-CI integrationhttps://patch-diff.githubusercontent.com/SelfHacked/bcftools/commit/a2dc76ebc18387e7b95116691f5421d41cc44328
https://patch-diff.githubusercontent.com/jkbonfield
jkbonfieldhttps://patch-diff.githubusercontent.com/SelfHacked/bcftools/commits?author=jkbonfield
a2dc76ehttps://patch-diff.githubusercontent.com/SelfHacked/bcftools/commit/a2dc76ebc18387e7b95116691f5421d41cc44328
https://patch-diff.githubusercontent.com/SelfHacked/bcftools/tree/a2dc76ebc18387e7b95116691f5421d41cc44328
Merge branch 'develop' of github.com:samtools/bcftools into develophttps://patch-diff.githubusercontent.com/SelfHacked/bcftools/commit/51492775b30ee441150ba51f1e519b10afb6dc95
https://patch-diff.githubusercontent.com/pd3
pd3https://patch-diff.githubusercontent.com/SelfHacked/bcftools/commits?author=pd3
5149277https://patch-diff.githubusercontent.com/SelfHacked/bcftools/commit/51492775b30ee441150ba51f1e519b10afb6dc95
https://patch-diff.githubusercontent.com/SelfHacked/bcftools/tree/51492775b30ee441150ba51f1e519b10afb6dc95
New -C option and `append-missing` logichttps://patch-diff.githubusercontent.com/SelfHacked/bcftools/commit/dc40b113d15ade803bc9a1b6431b63cb600401d4
https://patch-diff.githubusercontent.com/pd3
pd3https://patch-diff.githubusercontent.com/SelfHacked/bcftools/commits?author=pd3
dc40b11https://patch-diff.githubusercontent.com/SelfHacked/bcftools/commit/dc40b113d15ade803bc9a1b6431b63cb600401d4
https://patch-diff.githubusercontent.com/SelfHacked/bcftools/tree/dc40b113d15ade803bc9a1b6431b63cb600401d4
Merge pull request #1337 from daviesrob/appveyor_imghttps://patch-diff.githubusercontent.com/SelfHacked/bcftools/commit/2ca17e583a6e4fe319f859b89d59be62c48b524b
https://patch-diff.githubusercontent.com/pd3
pd3https://patch-diff.githubusercontent.com/SelfHacked/bcftools/commits?author=pd3
2ca17e5https://patch-diff.githubusercontent.com/SelfHacked/bcftools/commit/2ca17e583a6e4fe319f859b89d59be62c48b524b
https://patch-diff.githubusercontent.com/SelfHacked/bcftools/tree/2ca17e583a6e4fe319f859b89d59be62c48b524b
Remove appveyor "only build develop" branch restrictionhttps://patch-diff.githubusercontent.com/SelfHacked/bcftools/commit/465a63c92413604d7c639f558cf1891f95af8f50
https://patch-diff.githubusercontent.com/daviesrob
daviesrobhttps://patch-diff.githubusercontent.com/SelfHacked/bcftools/commits?author=daviesrob
465a63chttps://patch-diff.githubusercontent.com/SelfHacked/bcftools/commit/465a63c92413604d7c639f558cf1891f95af8f50
https://patch-diff.githubusercontent.com/SelfHacked/bcftools/tree/465a63c92413604d7c639f558cf1891f95af8f50
Upgrade AppVeyor imagehttps://patch-diff.githubusercontent.com/SelfHacked/bcftools/commit/808ced9ae2bb7d0939ed701199fbf876af0d0634
https://patch-diff.githubusercontent.com/daviesrob
daviesrobhttps://patch-diff.githubusercontent.com/SelfHacked/bcftools/commits?author=daviesrob
808ced9https://patch-diff.githubusercontent.com/SelfHacked/bcftools/commit/808ced9ae2bb7d0939ed701199fbf876af0d0634
https://patch-diff.githubusercontent.com/SelfHacked/bcftools/tree/808ced9ae2bb7d0939ed701199fbf876af0d0634
When first base of the reference genome is deleted,https://patch-diff.githubusercontent.com/SelfHacked/bcftools/commit/9c15769118cfc2e9c91813b563979eba7afc75c0
https://patch-diff.githubusercontent.com/pd3
pd3https://patch-diff.githubusercontent.com/SelfHacked/bcftools/commits?author=pd3
9c15769https://patch-diff.githubusercontent.com/SelfHacked/bcftools/commit/9c15769118cfc2e9c91813b563979eba7afc75c0
https://patch-diff.githubusercontent.com/SelfHacked/bcftools/tree/9c15769118cfc2e9c91813b563979eba7afc75c0
Append version and command line to the header unless --no-version is givenhttps://patch-diff.githubusercontent.com/SelfHacked/bcftools/commit/feb1ffc19abb4d30e1cc86002f49b47d6c3377b1
https://patch-diff.githubusercontent.com/pd3
pd3https://patch-diff.githubusercontent.com/SelfHacked/bcftools/commits?author=pd3
feb1ffchttps://patch-diff.githubusercontent.com/SelfHacked/bcftools/commit/feb1ffc19abb4d30e1cc86002f49b47d6c3377b1
https://patch-diff.githubusercontent.com/SelfHacked/bcftools/tree/feb1ffc19abb4d30e1cc86002f49b47d6c3377b1
Revise MAF definition for multiallelic sites,https://patch-diff.githubusercontent.com/SelfHacked/bcftools/commit/f57920e56bd919a26ad6ce8d55558eebe078f4cb
https://patch-diff.githubusercontent.com/pd3
pd3https://patch-diff.githubusercontent.com/SelfHacked/bcftools/commits?author=pd3
f57920ehttps://patch-diff.githubusercontent.com/SelfHacked/bcftools/commit/f57920e56bd919a26ad6ce8d55558eebe078f4cb
https://patch-diff.githubusercontent.com/SelfHacked/bcftools/tree/f57920e56bd919a26ad6ce8d55558eebe078f4cb
Bug fix: do add the NOVELGT annotation when requestedhttps://patch-diff.githubusercontent.com/SelfHacked/bcftools/commit/67c95eeff392d01fce04df2d8c802fe41401c734
https://patch-diff.githubusercontent.com/pd3
pd3https://patch-diff.githubusercontent.com/SelfHacked/bcftools/commits?author=pd3
67c95eehttps://patch-diff.githubusercontent.com/SelfHacked/bcftools/commit/67c95eeff392d01fce04df2d8c802fe41401c734
https://patch-diff.githubusercontent.com/SelfHacked/bcftools/tree/67c95eeff392d01fce04df2d8c802fe41401c734
Merge version number bump and NEWS file from masterhttps://patch-diff.githubusercontent.com/SelfHacked/bcftools/commit/87d355ef17983258eaa24daa158247b199295a0e
https://patch-diff.githubusercontent.com/valeriuo
valeriuohttps://patch-diff.githubusercontent.com/SelfHacked/bcftools/commits?author=valeriuo
87d355ehttps://patch-diff.githubusercontent.com/SelfHacked/bcftools/commit/87d355ef17983258eaa24daa158247b199295a0e
https://patch-diff.githubusercontent.com/SelfHacked/bcftools/tree/87d355ef17983258eaa24daa158247b199295a0e
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