… 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