Allow a "remove tag" operation followed by an "add the same tag" #1234
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pd3
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Feb 16, 2021
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Addresses issue 1414, not 1408 (similarly in the commit message). |
Fixes samtools/bcftools#1414 (bcftools annotate can segfault when --remove and --annotations used at once)
daviesrob
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Rebased to pick up the AppVeyor test fix, and correct the link in the commit message. |
clrpackages
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Jul 6, 2021
… 1.12
James Bonfield (2):
Add Cirrus-CI integration
Update .travis/clone to match Samtools.
John Marshall (17):
Use #include <assert.h> in source files that use assert()
Spelling corrections [minor]
Find bash via $PATH rather than hard-coding /bin/bash
Don't add hard-coded -ldl if configure was used
Fix Illumos build: don't use -pthread, other miscellanea
Fix convert bug and avoid other new Clang warnings
Fix Makefile dependencies for new gtcheck code
Rename bam_mpileup() to avoid clash with samtools's equivalent
Reformat NEWS to be legible on an 80-column terminal
Install misc/gff2gff.py and fix its #! to use python3
Various user-visible typo fixes
Remove generated test/*.fa.fai files
Include <strings.h> directly where needed
merge_format_string: Enlarge array for BCF_VL_A/BCF_VL_R too
Reformat NEWS to be legible on an 80-column terminal
Update Makefile dependencies; include <strings.h> directly where needed
Fix typo so MinGW users' $CPPFLAGS aren't ignored
Nicholas Knoblauch (1):
remove error before switch when fmt->type!=int8_t
Petr Danecek (174):
Minor: add explanatory comment
Add new --keep-duplicates option
Add new -a, --absent option.
Add new ad-bias -c, --clean-vcf option
Prevent segfault when INFO fields are present, unpack needs to be called
Fix bug in gVCF merging
Add new %N_PASS(..) formatting expression
Add check for duplicate and conflicting trios
Add a warning note to prevent problems like #1070
Improve error message on failed plugin dlopen. Resolves #1135
Make --SnpGap optionally filter also SNPs close to other types. Resolves #1126
Add support for multisample output and sample renaming
Fix a typo, add forgotten const format string to printf
Fix bug in splitting which leads in a corrupt FORMAT output
Several roh fixes
New --keep-sum option. Resolves #360
Fix #1149
Add a simple test for gtcheck
Rename the option `--output-file` to `--output` to make it consistent across bcftools commands.
Prevent segfault if no input file passed to +fill-tags
Overlapping deletions must not be forgotten in subsequent records with -a N.
Determine the case of the fasta sequence locally,
Fix a small memory leak
Fix in gvcf merging
Remove unused test output files
Add tests for 7a131a27
Updated INSTALL, see #1172
Plugins must not choke on the stdin "-" file name substitute. Fixes #1165
Add SMPL_*/S* family of functions that evaluate within rather than across all samples. Resolves #1180
Remove GSL dependant parts from travis dependencies
[NEWS] Support transfer of ID and FILTER to INFO by `annotate`
Support also multiple `annotate -l tag:type` options at the same time. Resolves #1198
Fix bug in the "row too big" detection when merging big VCFs
Update severity scale
Migrate plot-roh.py to python3
Experimental: Allow overlapping CDS to support ribosomal slippage. Resolves (partially) #1208
Extend documentation and print a warning when unintuitive string comparison is requested. Resolves #1212
Minor improvement in -R description
Add minor checks to keep compiler happy
Minor improvement in -R description
[NEWS] Extend +prune to allow annotating with various LD metrics,
Add support for INFO/END and INFO/TYPE
[NEWS] Major revamp of gtcheck
Check version of all plugins, regardless if they use init() or run()
Make --vcf-id work also in the direction to VCF. Fixes #1217
Minor documentation update
New -p/-P options
Fix an incorrect sanity check; Make the code a few % faster for huge comparisons (cross check on 32k samples)
Filling in END or TYPE does not require GT
New F_MISSING annotation supported by fill-tags
Two minor documentation updates
Whoopsy, there is also division which is not a commutative operator. Fixes #1224
Add forgotten test files
New --pairs option plus experimental --distinctive-sites
Make -i/-e functions aware that sample subset might have been requested
Make the --homs-only option work again. Randomize --distinctive-sites
Add tests for --distinctive-sites, update documentation, fix a major bug in external sorting, add tests
Print details about failed jobs on screen so that they appear in travis outputs
Make test transferable across platforms
Reduce required memory
Speed up and simplify the code by precomputing per-sample dosages and using bitwise comparisons for ambiguous PLs
New --use-likelihoods option for more accurate comparisons
Leave no temporary files behind even when killed
Docs: emphasize once more the difference between -r/-R and -t/-T
Make the new -l option the default and change it into more intuitive -e
Fix a silly typo: memcpy, not memset in the windows branch
Push forgotten update of tests
Add check for actual existence of perl library. Resolves #1171
Hacky solution to #1232
Fix the windows branch
Prevent segfault on first block. Fixes #1245
A better way of preserving LIBS integrity and remove bashism from configure.ac
Update man page
New +split -G option. Resolves #1240
[Minor] comment about the origin of a harmless compiler warning
New `merge --no-index` option which allows to merge unindexed files. (PR #1253)
Support for listing of uninformative sites, adds `-m u` and renames `-m s` to `-m c`
Account for commutative comparison operators, can't make this shortcut in code as in 68c8aba.
Add link to more documentation
Make `annotate -TAG/+TAG` work also with FORMAT fields.
Extend the man page to help prevent mistakes as in #1268
Informative error message on -x TAG w/o INFO or FORMAT prefix
Add default types for VEP subfields and make `-c -` to extract all subfields into INFO tags in one go.
Local alleles merging, produce LAA and LPL when requested.
Delete messed up test files
Fix a bug in localized merge of Number=A tags; Fix messed up test files
More informative error message; Fix minor memory leak
Fix minor memory leaks in split-vep pugin
Prevent segfault on REF-only positions with ALT="." and -I. Fixes #1273
Minor usage page update
Update headers when appropriate when merging with the join info rule. Fixes #1282
Breaking change in filtering expressions on FILTER column.
Provide a better diagnostic error message. Resolves #1280
Add missing consequence type \"non_coding\". Resolves #1292
Make `norm -c s` fix non-ACGTN REF and ALT bases. Resolves #473
Prevent buffer overrun on symbolic <DEL> alleles, driven by INFO/END. Replaces #1295
Extend dc26549f6, handle cases where a SNP is immediately followed by a <DEL>. See also #1295
Check for failure to read the --samples file; check for bgzf vs other compression types. Resolves #1288
Give informative error when FORMAT not present but adding of --samples requested
Extend the support for the `-c =TAG` and `--merge-logic` features
Add gff2gff.py script contributed by @flashton2003 in #530
Fix bug in `norm -c s`
Minor clarification of the discordance calculation
Update NEWS
HWE requires customized merging. (Note this cannot be done exactly, is an approximation.) Fixes #1296
Minor man page fix, wrong future version number was predicted
Unless -x is given, output also sites with no CSQ annotation. Resolves #1303
Minor usage text clarification
Bug fix: do add the NOVELGT annotation when requested
Revise MAF definition for multiallelic sites,
Append version and command line to the header unless --no-version is given
When first base of the reference genome is deleted,
New -C option and `append-missing` logic
Clarify how --n-matches works, allow to choose all samples
Make F_MISSING work for sites with many ALT alleles. Fixes #1343
Do not phase genotypes that are not phased with `concat -l`. Fixes #1346
Make an assumption about <DEL> start when strlen(REF)!=1. Resolves #1319
Add new `annotate --rename-annots` option to help fix broken VCFs. Resolves #1335
More informative error message. Resolves #1128
Prevent internal dropping of samples on VCF input and VCF/BCF output
Add missing gtcheck tests
Changes to QUAL and ts/tv plotting stats
Add new optional tag by `mpileup -a FORMAT/QS`
[NEWS] Major revamp of `bcftools +trio-dnm`
[NEWS] Revamp of `bcftools call -G`
Rename trio-dnm to trio-dnm2 to avoid confusion
Add explicit --group-samples-tag option. Resolves #1370
Clarification of merge -R behavior. Resolves #1374
Update mpileup test to reflect samtools/htslib@481bd22
Make trio-dnm2 output log-scaled scores by default;
Autodetected output file type from the output file suffix (e.g. .bcf, .vcf, .vcf.gz)
Make `merge -R` behavior consistent with other commands and
Add new `+prune -N, --nsites-per-win-mode` mode. Resolves #1050
Add new --mark-del, --mark-ins, and --mark-snv options. Resolves #1381 and #1170
Add --random-seed option to make tests reproducible
Switch to PCG to ensure test reproducibility across platforms
Add forgotten \0 string termination
More informative error message, see #294
Make the behavior of --hapsample and --hapsample2vcf consistent
Make +split-vep transcript selection work also on the raw CSQ/BCSQ annotation.
Add a new `consensus --mask-with` option. Resolves #1382
Use hts_[sl]rand() functions instead of introducing PCG. Reverts and replaces 61bab7529f.
Throw an error if -i/-e expression is given multiple times. Prevents errors #1388
Support for IUPAC codes in insertions and MNVs, plus a new -H I option. Resolves #1241,#1393
Indicate which of the alleles is de novo and report the corresponding VAF
User proper-sized max int value and avoid a compiler warning
Autodetect file type, the `view` command was missed by 7496b17
Do not recommendation `mpileup -C 50`, its efficacy has not been proved
Check the source tag type
Fix N_PASS and F_PASS to behave according to expectation
Replace special characters with underscore when generating file names
Make `consensus -I` and `-H I` work with arbitrary ploidy. Resolves #1400
Fix wrong check of strchr() return value, avoid segfault with -u tag=DNG
Tests for #1414. The pullrequest samtools/htslib#1234 should fix
Fix transfer of ID
Throw an error on incorrectly formatted --AF-file files. Likely resolves #1417
Support for FORMAT/VAF,VAF1 annotations. Resolves #1422
Fix a typo, thanks to @tbenavi1. Resolves #1424
Add new --atomize and --old-rec-tag options
Prevent invalid memory access
Update man page and INSTALL instructions
Fix a signed comparison as pointed by samtools/bcftools#1400 (comment)
Make warnings into errors for automated tests
Print the maximum number of CSQs per sample once finished.
Fix minor typos in NEWS
Happy New Year!
Comment out unused function to prevent `./configure --enable-werror` failures on tests platforms
Fix incorrect output when query combines -s/-S with -i/-e
Update documentation to mention GT="mis" as well. See also #1435
The `csq --ncsq` option was handled incorrectly,
Show full diff of failed tests to help diagnose problems on automated CI platforms
Replace sed one-liner with perl as substitution with newline works differently on sed implementation on MAC OS
Tests for #1441, fail until samtools/htslib#1254 is merged
Allow to specify the default ploidy explicitly via `--ploidy 2`. Resolves #1436
Rob Davies (7):
Add note about how to get gsl-dev on alpine [minor]
Don't try to return a value (albeit void) from a void function.
Upgrade AppVeyor image
Remove appveyor "only build develop" branch restriction
Update CI test configuration to recurse htslib submodules
Continuous integration test updates
Add more make targets to use when building HTSlib with BCFtools
Valeriu Ohan (2):
Check for null header pointer.
Update copyright.
freeseek (2):
add scatter plugin
added the ability for the mendelian plugin to read ped files and output VCFs with mendelian errors annotation
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Fixes samtools/bcftools#1414