GitHub / samtools/bcftools / commits
| SHA | Message | Author | Date | Stats |
|---|---|---|---|---|
| e250385b | Make the advertised default for `-t, --threshold` match the implementation. | Petr Danecek <p****3@s****k> | 3 months ago | |
| f5e6080e | Print a warning when `call -m` is used w/o -v | Petr Danecek <p****3@s****k> | 3 months ago | |
| 719451e5 | Convert ambiguous IUPAC bases according to the VCF specification. Resolves #2551 | Petr Danecek <p****3@s****k> | 3 months ago | |
| c4617c5c | Fixed calculation of MAC and MAF in `-i/-e` filtering expressions | Petr Danecek <p****3@s****k> | 3 months ago | |
| 90e60256 | Add a new -G, --greedy option | Petr Danecek <p****3@s****k> | 3 months ago | |
| b308be54 | [Minor] fix typos, add comments | Petr Danecek <p****3@s****k> | 3 months ago | |
| e0ec6ab0 | Stage text output through canonical VCF consequences | Petr Danecek <p****3@s****k> | 4 months ago | |
| 6967378c | Make kput_vcsq() a read-only formatter | Petr Danecek <p****3@s****k> | 4 months ago | |
| da89859c | Add forgotten test file | Petr Danecek <p****3@s****k> | 4 months ago | |
| 6dbd8fef | Fix sex handling and report non-error trio states | Petr Danecek <p****3@s****k> | 4 months ago | |
| eecce29d | Fix a start_lost issue in haplotype mode | Petr Danecek <p****3@s****k> | 4 months ago | |
| 34a60054 |
Add a CONTRIBUTING file
Signed-off-by: Rob Davies <r****t@s****k> |
Rob Davies <r****t@s****k> | 4 months ago | |
| 0b2fa4ec |
Fix warning about discarding const in init_index2()
Signed-off-by: Rob Davies <r****t@s****k> |
Rob Davies <r****t@s****k>
Committed by: daviesrob <r****t@s****k> |
4 months ago | |
| 16b94629 | Add GSL_LIBS to W32_PLUGIN_LIBS |
Rob Davies <r****t@s****k>
Committed by: Petr Danecek <p****3@s****k> |
4 months ago | |
| 7fd0dfb3 | Remove usage of sprintf() |
Rob Davies <r****t@s****k>
Committed by: Petr Danecek <p****3@s****k> |
4 months ago | |
| ecfca758 | Add Github actions builds for Linux and Mac OS (needs htslib#2000) |
Rob Davies <r****t@s****k>
Committed by: Petr Danecek <p****3@s****k> |
4 months ago | |
| d9375776 | Fix erroneous INFO/END recalculation; New --no-realign option | Petr Danecek <p****3@s****k> | 5 months ago | |
| 381e6937 | Extend per-population filtering | Petr Danecek <p****3@s****k> | 5 months ago | |
| b64ebe7b | Revert a bug introduced by PR #2533 | Petr Danecek <p****3@s****k> | 5 months ago | |
| 8cd70c91 | Check for faidx_fetch failure, picked from #2536 | Petr Danecek <p****3@s****k> | 5 months ago | |
| 99f0afb1 | Minor code tightening | Petr Danecek <p****3@s****k> | 5 months ago | |
| f8de1ed5 | Add test for #2526 | Petr Danecek <p****3@s****k> | 5 months ago | |
| da315c5f | Allow annotation of Number=A,R INFO tags from tab-delimited files when allele... | Petr Danecek <p****3@s****k> | 5 months ago | |
| c9224d0c | Update test | Petr Danecek <p****3@s****k> | 5 months ago | |
| 529d2ce5 | Update test | Petr Danecek <p****3@s****k> | 5 months ago | |
| 449a8af0 | Add part #1 of #2524, adding a test and fixing the introduced bug | Petr Danecek <p****3@s****k> | 5 months ago | |
| 9be83679 | Add new `-m exact` merging mode. Resolves #2498 | Petr Danecek <p****3@s****k> | 5 months ago | |
| 89dfe49f | Make test sort use the same order on windows and linux | Petr Danecek <p****3@s****k> | 5 months ago | |
| e4dee24d | Remove useless check to prevent triggering of `-Werror -Wformat=2` failure wi... | Petr Danecek <p****3@s****k> | 5 months ago | |
| d73ed56c | Add test for #2520 | Petr Danecek <p****3@s****k> | 5 months ago | |
| 78c13cd8 | Update tests | Petr Danecek <p****3@s****k> | 5 months ago | |
| 10b80ed1 | merge Merge branch 'develop' of github.com:samtools/bcftools into develop | Petr Danecek <p****3@s****k> | 5 months ago | |
| 60fad50b | Accept #2519 with additional fixes and polishes | Petr Danecek <p****3@s****k> | 5 months ago | |
| adbf93ef | Make a better random seed, add ##bcftools_plugin_prune_RandomSeed into the he... | Petr Danecek <p****3@s****k> | 5 months ago | |
| 391af41d | Add missing test file | Petr Danecek <p****3@s****k> | 5 months ago | |
| f0930ccf | Remove forgotten debugging output | Petr Danecek <p****3@s****k> | 5 months ago | |
| e4b8ecf0 | Fix per-sample statistics | Petr Danecek <p****3@s****k> | 5 months ago | |
| 48d3e75c | Fix a typo | Petr Danecek <p****3@s****k> | 5 months ago | |
| 8307239d | Fix trailing N_REF_PAD copy offset in spliced reference | Petr Danecek <p****3@s****k> | 5 months ago | |
| d2ed9a6e | Fix OOB codon | Petr Danecek <p****3@s****k> | 5 months ago | |
| 5f4fd434 | Add forgotten test file | Petr Danecek <p****3@s****k> | 5 months ago | |
| c57cdd89 | merge Merge branch 'develop' of github.com:samtools/bcftools into develop | Petr Danecek <p****3@s****k> | 5 months ago | |
| 83dad305 | Fix a bug in annotation renaming via `--rename-annots` and `-c NEW:=OLD`, | Petr Danecek <p****3@s****k> | 5 months ago | |
| 47ea4412 | Replace assert() with proper error handling for user-triggerable conditions |
sirus20x6 <s****6@u****m>
Committed by: Petr Danecek <p****3@s****k> |
5 months ago | |
| 1860cb6b | Fix memset bugs in bam2bcf_iaux.c and bam2bcf.c |
sirus20x6 <s****6@u****m>
Committed by: Petr Danecek <p****3@s****k> |
5 months ago | |
| 0039c202 | Fix 10 assorted medium-severity bugs across multiple files |
sirus20x6 <s****6@u****m>
Committed by: Petr Danecek <p****3@s****k> |
5 months ago | |
| 0486a686 | Fix three bugs in bam2bcf indel calling |
sirus20x6 <s****6@u****m>
Committed by: Petr Danecek <p****3@s****k> |
5 months ago | |
| a49df0c4 | Fix two bugs in regidx.c: OOB array access and double-free |
sirus20x6 <s****6@u****m>
Committed by: Petr Danecek <p****3@s****k> |
5 months ago | |
| 944cebd4 | Fix type mismatch in ccall.c and division by zero in mcall.c |
sirus20x6 <s****6@u****m>
Committed by: Petr Danecek <p****3@s****k> |
5 months ago | |
| ceab492c | Fix two bugs in tabix.c: dead code and missing NULL check |
sirus20x6 <s****6@u****m>
Committed by: Petr Danecek <p****3@s****k> |
5 months ago | |
| bf816300 | Fix multiple bugs in filter engine and vcffilter |
sirus20x6 <s****6@u****m>
Committed by: Petr Danecek <p****3@s****k> |
5 months ago | |
| 39743393 | Fix three bugs in vcfconvert.c |
sirus20x6 <s****6@u****m>
Committed by: Petr Danecek <p****3@s****k> |
5 months ago | |
| 9e015117 | Fix three bugs in vcfmerge FORMAT field handling |
sirus20x6 <s****6@u****m>
Committed by: Petr Danecek <p****3@s****k> |
5 months ago | |
| 3f8280cb | Fix wrong array used for float missing-value in split_format_numeric |
sirus20x6 <s****6@u****m>
Committed by: Petr Danecek <p****3@s****k> |
5 months ago | |
| c0a0bbde | Fix wrong loop variable in family trio sample remapping |
sirus20x6 <s****6@u****m>
Committed by: Petr Danecek <p****3@s****k> |
5 months ago | |
| db17826e | merge Merge branch 'develop' of pd3-github:samtools/bcftools into develop | Petr Danecek <p****3@s****k> | 5 months ago | |
| 0c238d11 | Fix a bug in splitting Type=String FORMAT fields via -a and -m | Petr Danecek <p****3@s****k> | 5 months ago | |
| 0b249f0d | Make --gvcf2vcf work around malformed gVCF records | Petr Danecek <p****3@s****k> | 5 months ago | |
| ff979251 | Add new --with-cAD option | Petr Danecek <p****3@s****k> | 5 months ago | |
| 09c045dd | Tighten faidx_fetch_seq check, can happen if wrong fasta is supplied | Petr Danecek <p****3@s****k> | 6 months ago | |
| 2857c7ec | Update NEWS | Petr Danecek <p****3@s****k> | 6 months ago | |
| f16f11f3 | merge Merge branch 'develop' of pd3-github:samtools/bcftools into develop | Petr Danecek <p****3@s****k> | 6 months ago | |
| dc19be58 | Fix prune behavior | Petr Danecek <p****3@s****k> | 6 months ago | |
| f33d1a36 | merge Merge branch 'develop' of github.com:samtools/bcftools into develop | Petr Danecek <p****3@s****k> | 6 months ago | |
| c3cd6dfa | Remove redundant test; Increase time limit to 15 min as tests run out of time | Petr Danecek <p****3@s****k> | 6 months ago | |
| ac0825e4 | merge Merge version number bump and NEWS file from master | Rob Davies <r****t@s****k> | 6 months ago | |
| ff1604d4 | merge Release 1.23.1 | Rob Davies <r****t@s****k> | 6 months ago | |
| 98c99a09 | Fix Windows trio-dnm3 tests. |
James Bonfield <j****b@s****k>
Committed by: Petr Danecek <p****3@s****k> |
6 months ago | |
| db566e75 | NEWS updates for point release | Rob Davies <r****t@s****k> | 6 months ago | |
| 16f2e71d | Clearer error message |
Matthieu Muffato <m****9@s****k>
Committed by: Petr Danecek <p****3@s****k> |
6 months ago | |
| 3b22f2fc | Directly invoke gunzip rather than the zless wrapper |
Matthieu Muffato <m****9@s****k>
Committed by: Petr Danecek <p****3@s****k> |
6 months ago | |
| 3167b5b1 |
Safer invocation of zless
Co-authored-by: Copilot <1****t@u****m> |
Matthieu Muffato <c****b@y****r>
Committed by: Petr Danecek <p****3@s****k> |
6 months ago | |
| 39fb59a4 |
Reference the right input file name
Co-authored-by: Copilot <1****t@u****m> |
Matthieu Muffato <c****b@y****r>
Committed by: Petr Danecek <p****3@s****k> |
6 months ago | |
| 75510af7 | Make test work on windows | Petr Danecek <p****3@s****k> | 6 months ago | |
| 8bbf8c7e | Remove unused code | Petr Danecek <p****3@s****k> | 6 months ago | |
| b4ae9434 | Fix failing test | Petr Danecek <p****3@s****k> | 6 months ago | |
| 94bc110e | minor: Update man page | Petr Danecek <p****3@s****k> | 6 months ago | |
| 9f37d74f | merge Merge branch 'develop' of github.com:samtools/bcftools into develop | Petr Danecek <p****3@s****k> | 6 months ago | |
| 478df308 | Add new --use-DMM model | Petr Danecek <p****3@s****k> | 6 months ago | |
| 29b75382 | Fix silent truncation when synced reader encounters I/O errors |
Giles Hall <g****s@b****g>
Committed by: Rob Davies <r****t@s****k> |
7 months ago | |
| 63e0b4f9 | Fix silent truncation when synced reader encounters I/O errors |
Giles Hall <g****s@b****g>
Committed by: Petr Danecek <p****3@s****k> |
7 months ago | |
| 34a49760 | Wrap ctype.h functions to avoid array subscript warnings |
Rob Davies <r****t@s****k>
Committed by: James Bonfield <j****b@s****k> |
7 months ago | |
| de0606d1 | Change sed regex to remove all 'redhat-hardened-ld*' entries from Perl options. | Rasmus Ory Nielsen <r****n@r****k> | 7 months ago | |
| b0a84690 | New -s, --samples option | Petr Danecek <p****3@s****k> | 8 months ago | |
| 638bee2d | merge Merge version number bump and NEWS file from master | Rob Davies <r****t@s****k> | 9 months ago | |
| 56e72e4c | merge Release 1.23 | Rob Davies <r****t@s****k> | 9 months ago | |
| ef01dee3 | Fix inadvertent variable length array |
Rob Davies <r****t@s****k>
Committed by: Andrew Whitwham <w****m@u****m> |
9 months ago | |
| 28a0c872 | Add test and a sanity check | Petr Danecek <p****3@s****k> | 10 months ago | |
| 48c3548a | Add test | Petr Danecek <p****3@s****k> | 10 months ago | |
| c3b7d7ed | Numerical functions, such as SUM(INFO/DP), in formatting expressions of query | Petr Danecek <p****3@s****k> | 10 months ago | |
| 8d73103c | Fix the option `-A, --all-fields`, it was not working properly and could lead... | Petr Danecek <p****3@s****k> | 10 months ago | |
| 3e3cab62 | Prevent count overflow in large genomes [minor] | Petr Danecek <p****3@s****k> | 10 months ago | |
| 5096c7ca | Fix JS libraries embedding for offline rendering |
Aleksei Vambol <7****l@u****m>
Committed by: Petr Danecek <p****3@s****k> |
10 months ago | |
| a26af0ed | Update test output to work with HTSlib Number= PR htslib#1874 |
Rob Davies <r****t@s****k>
Committed by: Petr Danecek <p****3@s****k> |
11 months ago | |
| f79d6307 | merge Merge branch 'develop' of github.com:samtools/bcftools into develop | Petr Danecek <p****3@s****k> | 11 months ago | |
| 46174323 | Throw an error, do not segfault (#2459) | Petr Danecek <p****3@s****k> | 11 months ago | |
| f383f465 | Make 60-char output when the buffer is flushed at the end | Petr Danecek <p****3@s****k> | 11 months ago | |
| dcd3658e | merge Merge branch 'develop' of pd3-github:samtools/bcftools into develop | Petr Danecek <p****3@s****k> | 11 months ago | |
| 6d691415 | Fix a bug which causes `consensus --absent` miss some absent positions | Petr Danecek <p****3@s****k> | 11 months ago | |
| c5a978f7 | Emphasize there is a difference when annotating from VCF/BCF vs tab-delimited... | Petr Danecek <p****3@s****k> | 11 months ago |