Loading .appveyor.yml 0 → 100644 +54 −0 Original line number Diff line number Diff line # version format. # you can use {branch} name in version format too # version: 1.0.{build}-{branch} version: 'vers.{build}' # branches to build branches: # Whitelist only: - develop # Blacklist except: - gh-pages # Do not build on tags (GitHub and BitBucket) skip_tags: true # Skipping commits affecting specific files (GitHub only). More details here: /docs/appveyor-yml #skip_commits: # files: # - docs/* # - '**/*.html' # We use Mingw/Msys, so use pacman for installs install: - set HOME=. - set MSYSTEM=MINGW64 - set PATH=C:/msys64/usr/bin;C:/msys64/mingw64/bin;%PATH% - set MINGWPREFIX=x86_64-w64-mingw32 - "sh -lc \"pacman -S --noconfirm --needed base-devel mingw-w64-x86_64-toolchain mingw-w64-x86_64-zlib mingw-w64-x86_64-bzip2 mingw-w64-x86_64-xz mingw-w64-x86_64-curl\"" # The user may have e.g. jkbonfield/bcftools branch FOO and an associated # jkbonfield/htslib branch FOO. If so use that related htslib, obtained by # munging $APPVEYOR_REPO_NAME. Otherwise we assume this is a PR only to # bcftools and should be linked against samtools(org)/htslib develop branch. clone_script: - "sh -lc \"if test x$APPVEYOR_PULL_REQUEST_HEAD_REPO_NAME != x ; then git clone --branch=$APPVEYOR_PULL_REQUEST_HEAD_REPO_BRANCH https://github.com/$APPVEYOR_PULL_REQUEST_HEAD_REPO_NAME $APPVEYOR_BUILD_FOLDER ; else false ; fi || git clone --branch=$APPVEYOR_REPO_BRANCH https://github.com/$APPVEYOR_REPO_NAME $APPVEYOR_BUILD_FOLDER\"" - "sh -lc \"git show-branch --sha1-name HEAD" - "sh -lc \"git clone --branch=$APPVEYOR_REPO_BRANCH https://github.com/`echo $APPVEYOR_REPO_NAME|sed 's#/bcftools#/htslib#'`.git $APPVEYOR_BUILD_FOLDER/htslib || git clone https://github.com/samtools/htslib.git $APPVEYOR_BUILD_FOLDER/htslib \"" - "sh -lc \"cd $APPVEYOR_BUILD_FOLDER/htslib && git show-branch --sha1-name HEAD\"" build_script: - set HOME=. - set MSYSTEM=MINGW64 - set PATH=C:/msys64/usr/bin;C:/msys64/mingw64/bin;%PATH% - "sh -lc \"(cd htslib; aclocal && autoheader && autoconf)\"" - "sh -lc \"aclocal && autoheader && autoconf && ./configure && make -j2\"" test_script: - set HOME=. - set MSYSTEM=MINGW64 - set PATH=C:/msys64/usr/bin;C:/msys64/mingw64/bin;%APPVEYOR_BUILD_FOLDER%/htslib;%PATH% - "sh -lc \"MSYS2_ARG_CONV_EXCL=* make test-plugins\"" LICENSE +23 −0 Original line number Diff line number Diff line Loading @@ -723,3 +723,26 @@ Public License instead of this License. But first, please read ----------------------------------------------------------------------------- LICENSE FOR VariantKey (https://github.com/Genomicsplc/variantkey) The MIT License Copyright (c) 2017-2018 GENOMICS plc Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. Makefile +73 −30 Original line number Diff line number Diff line Loading @@ -23,8 +23,10 @@ # DEALINGS IN THE SOFTWARE. CC = gcc AR = ar RANLIB = ranlib CPPFLAGS = CFLAGS = -g -Wall -Wc++-compat -O2 CFLAGS = -g -Wall -O2 LDFLAGS = LIBS = Loading @@ -36,11 +38,12 @@ OBJS = main.o vcfindex.o tabix.o \ vcfstats.o vcfisec.o vcfmerge.o vcfquery.o vcffilter.o filter.o vcfsom.o \ vcfnorm.o vcfgtcheck.o vcfview.o vcfannotate.o vcfroh.o vcfconcat.o \ vcfcall.o mcall.o vcmp.o gvcf.o reheader.o convert.o vcfconvert.o tsv2vcf.o \ vcfcnv.o HMM.o vcfplugin.o consensus.o ploidy.o bin.o hclust.o version.o \ vcfcnv.o HMM.o consensus.o ploidy.o bin.o hclust.o version.o \ regidx.o smpl_ilist.o csq.o vcfbuf.o \ mpileup.o bam2bcf.o bam2bcf_indel.o bam_sample.o \ vcfsort.o \ vcfsort.o cols.o \ ccall.o em.o prob1.o kmin.o # the original samtools calling PLUGIN_OBJS = vcfplugin.o prefix = /usr/local exec_prefix = $(prefix) Loading Loading @@ -73,11 +76,18 @@ MISC_SCRIPTS = \ misc/vcfutils.pl TEST_PROGRAMS = test/test-rbuf test/test-regidx all: $(PROGRAMS) $(TEST_PROGRAMS) plugins ALL_CPPFLAGS = -I. $(HTSLIB_CPPFLAGS) $(CPPFLAGS) ALL_LDFLAGS = $(HTSLIB_LDFLAGS) $(LDFLAGS) ALL_LIBS = -lz -ldl $(LIBS) ALL_LIBS = -lz $(DL_LIBS) $(LIBS) all: $(PROGRAMS) $(TEST_PROGRAMS) plugins EXTRA_CPPFLAGS = GSL_LIBS = # On windows, plugins need to be fully linked. This adds the extra libraries # needed. Defined here so config.mk can override it. W32_PLUGIN_LIBS = libbcftools.a $(HTSLIB_DLL) $(ALL_LIBS) # Usually config.mk and config.h are generated by running configure # or config.status, but if those aren't used create defaults here. Loading @@ -88,12 +98,12 @@ config.h: echo '/* Basic config.h generated by Makefile */' > $@ ifneq "$(PLUGINS_ENABLED)" "no" echo '#define ENABLE_BCF_PLUGINS 1' >> $@ echo '#define PLUGIN_EXT ".so"' >> $@ echo '#define PLUGIN_EXT "$(PLUGIN_EXT)"' >> $@ endif include config.mk PACKAGE_VERSION = 1.9 PACKAGE_VERSION = 1.10 # If building from a Git repository, replace $(PACKAGE_VERSION) with the Git # description of the working tree: either a release tag with the same value Loading Loading @@ -134,14 +144,15 @@ ifdef USE_GPL GSL_LIBS ?= -lgsl -lcblas endif bcftools: $(OBJS) $(HTSLIB) $(CC) $(DYNAMIC_FLAGS) -pthread $(ALL_LDFLAGS) -o $@ $(OBJS) $(HTSLIB_LIB) -lm $(ALL_LIBS) $(GSL_LIBS) $(PERL_LIBS) print-%: @echo '$*=$($*)' # Plugin rules ifneq "$(PLUGINS_ENABLED)" "no" PLUGINC = $(foreach dir, plugins, $(wildcard $(dir)/*.c)) PLUGINS = $(PLUGINC:.c=$(PLUGIN_EXT)) PLUGINM = $(PLUGINC:.c=.mk) OBJS += $(PLUGIN_OBJS) ifneq "$(origin PLATFORM)" "file" PLATFORM := $(shell uname -s) Loading @@ -149,12 +160,35 @@ endif ifeq "$(PLATFORM)" "Darwin" $(PLUGINS): | bcftools PLUGIN_FLAGS = -bundle -bundle_loader bcftools -Wl,-undefined,dynamic_lookup DL_LIBS = else ifeq "$(PLATFORM)" "CYGWIN" $(PLUGINS): | bcftools PLUGIN_FLAGS = -fPIC -shared PLUGIN_LIBS = $(W32_PLUGIN_LIBS) DL_LIBS = -ldl else ifneq "$(filter MINGW% MSYS%,$(PLATFORM))" "" DYNAMIC_FLAGS = $(PLUGINS): | bcftools PLUGIN_FLAGS = -fPIC -shared -Wl,-export-all-symbols PLUGIN_LIBS = $(W32_PLUGIN_LIBS) # On windows, plugins need to be fully linked, including bcftools_version() symbol # from the application they will be loaded into. DL_LIBS = else PLUGIN_FLAGS = -fPIC -shared DL_LIBS = -ldl endif libbcftools.a: $(OBJS) @-rm -f $@ $(AR) -rc $@ $(OBJS) -$(RANLIB) $@ vcfplugin.o: EXTRA_CPPFLAGS += -DPLUGINPATH='"$(pluginpath)"' %.dll %.cygdll: %.c version.h version.c libbcftools.a $(HTSLIB_DLL) $(CC) $(PLUGIN_FLAGS) $(CFLAGS) $(ALL_CPPFLAGS) $(EXTRA_CPPFLAGS) $(LDFLAGS) -o $@ version.c $< $(PLUGIN_LIBS) %.so: %.c version.h version.c $(CC) $(PLUGIN_FLAGS) $(CFLAGS) $(ALL_CPPFLAGS) $(EXTRA_CPPFLAGS) $(LDFLAGS) -o $@ version.c $< $(LIBS) Loading @@ -172,10 +206,14 @@ test check: test-no-plugins endif # PLUGINS_ENABLED bcftools: $(OBJS) $(HTSLIB) $(CC) $(DYNAMIC_FLAGS) -pthread $(ALL_LDFLAGS) -o $@ $(OBJS) $(HTSLIB_LIB) -lm $(ALL_LIBS) $(GSL_LIBS) $(PERL_LIBS) plugins: $(PLUGINS) bcftools_h = bcftools.h $(htslib_hts_defs_h) $(htslib_vcf_h) call_h = call.h $(htslib_vcf_h) $(htslib_synced_bcf_reader_h) vcmp.h variantkey_h = variantkey.h hex.h convert_h = convert.h $(htslib_vcf_h) tsv2vcf_h = tsv2vcf.h $(htslib_vcf_h) filter_h = filter.h $(htslib_vcf_h) Loading @@ -189,41 +227,42 @@ bam2bcf_h = bam2bcf.h $(htslib_hts_h) $(htslib_vcf_h) bam_sample_h = bam_sample.h $(htslib_sam_h) main.o: main.c $(htslib_hts_h) config.h version.h $(bcftools_h) vcfannotate.o: vcfannotate.c $(htslib_vcf_h) $(htslib_synced_bcf_reader_h) $(htslib_kseq_h) $(htslib_khash_str2int_h) $(bcftools_h) vcmp.h $(filter_h) $(convert_h) $(smpl_ilist_h) $(htslib_khash_h) vcfannotate.o: vcfannotate.c $(htslib_vcf_h) $(htslib_synced_bcf_reader_h) $(htslib_kseq_h) $(htslib_khash_str2int_h) $(bcftools_h) vcmp.h $(filter_h) $(convert_h) $(smpl_ilist_h) regidx.h $(htslib_khash_h) vcfplugin.o: vcfplugin.c config.h $(htslib_vcf_h) $(htslib_synced_bcf_reader_h) $(htslib_kseq_h) $(htslib_khash_str2int_h) $(bcftools_h) vcmp.h $(filter_h) vcfcall.o: vcfcall.c $(htslib_vcf_h) $(htslib_kfunc_h) $(htslib_synced_bcf_reader_h) $(htslib_khash_str2int_h) $(bcftools_h) $(call_h) $(prob1_h) $(ploidy_h) $(gvcf_h) vcfconcat.o: vcfconcat.c $(htslib_vcf_h) $(htslib_synced_bcf_reader_h) $(htslib_kseq_h) $(htslib_bgzf_h) $(htslib_tbx_h) $(bcftools_h) vcfcall.o: vcfcall.c $(htslib_vcf_h) $(htslib_kfunc_h) $(htslib_synced_bcf_reader_h) $(htslib_khash_str2int_h) $(bcftools_h) $(call_h) $(prob1_h) $(ploidy_h) $(gvcf_h) regidx.h $(vcfbuf_h) vcfconcat.o: vcfconcat.c $(htslib_vcf_h) $(htslib_synced_bcf_reader_h) $(htslib_kseq_h) $(htslib_bgzf_h) $(htslib_tbx_h) $(htslib_thread_pool_h) $(bcftools_h) vcfconvert.o: vcfconvert.c $(htslib_faidx_h) $(htslib_vcf_h) $(htslib_bgzf_h) $(htslib_synced_bcf_reader_h) $(htslib_vcfutils_h) $(htslib_kseq_h) $(bcftools_h) $(filter_h) $(convert_h) $(tsv2vcf_h) vcffilter.o: vcffilter.c $(htslib_vcf_h) $(htslib_synced_bcf_reader_h) $(htslib_vcfutils_h) $(bcftools_h) $(filter_h) rbuf.h vcfgtcheck.o: vcfgtcheck.c $(htslib_vcf_h) $(htslib_synced_bcf_reader_h) $(htslib_vcfutils_h) $(bcftools_h) hclust.h vcfindex.o: vcfindex.c $(htslib_vcf_h) $(htslib_tbx_h) $(htslib_kstring_h) $(htslib_bgzf_h) $(bcftools_h) vcfisec.o: vcfisec.c $(htslib_vcf_h) $(htslib_synced_bcf_reader_h) $(htslib_vcfutils_h) $(bcftools_h) $(filter_h) vcfisec.o: vcfisec.c $(htslib_vcf_h) $(htslib_synced_bcf_reader_h) $(htslib_vcfutils_h) $(htslib_hts_os_h) $(bcftools_h) $(filter_h) vcfmerge.o: vcfmerge.c $(htslib_vcf_h) $(htslib_synced_bcf_reader_h) $(htslib_vcfutils_h) $(htslib_faidx_h) regidx.h $(bcftools_h) vcmp.h $(htslib_khash_h) vcfnorm.o: vcfnorm.c $(htslib_vcf_h) $(htslib_synced_bcf_reader_h) $(htslib_faidx_h) $(htslib_khash_str2int_h) $(bcftools_h) rbuf.h vcfquery.o: vcfquery.c $(htslib_vcf_h) $(htslib_synced_bcf_reader_h) $(htslib_khash_str2int_h) $(htslib_vcfutils_h) $(bcftools_h) $(filter_h) $(convert_h) vcfroh.o: vcfroh.c $(htslib_vcf_h) $(htslib_synced_bcf_reader_h) $(htslib_kstring_h) $(htslib_kseq_h) $(htslib_bgzf_h) $(bcftools_h) HMM.h $(smpl_ilist_h) $(filter_h) vcfcnv.o: vcfcnv.c $(htslib_vcf_h) $(htslib_synced_bcf_reader_h) $(htslib_kstring_h) $(htslib_kfunc_h) $(htslib_khash_str2int_h) $(bcftools_h) HMM.h rbuf.h vcfsom.o: vcfsom.c $(htslib_vcf_h) $(htslib_synced_bcf_reader_h) $(htslib_vcfutils_h) $(bcftools_h) vcfsort.o: vcfsort.c $(htslib_vcf_h) $(htslib_kstring_h) kheap.h $(bcftools_h) vcfsom.o: vcfsom.c $(htslib_vcf_h) $(htslib_synced_bcf_reader_h) $(htslib_vcfutils_h) $(htslib_hts_os_h) $(bcftools_h) vcfsort.o: vcfsort.c $(htslib_vcf_h) $(htslib_kstring_h) $(htslib_hts_os_h) kheap.h $(bcftools_h) vcfstats.o: vcfstats.c $(htslib_vcf_h) $(htslib_synced_bcf_reader_h) $(htslib_vcfutils_h) $(htslib_faidx_h) $(bcftools_h) $(filter_h) bin.h vcfview.o: vcfview.c $(htslib_vcf_h) $(htslib_synced_bcf_reader_h) $(htslib_vcfutils_h) $(bcftools_h) $(filter_h) $(htslib_khash_str2int_h) reheader.o: reheader.c $(htslib_vcf_h) $(htslib_bgzf_h) $(htslib_tbx_h) $(htslib_kseq_h) $(htslib_thread_pool_h) $(bcftools_h) $(khash_str2str_h) reheader.o: reheader.c $(htslib_vcf_h) $(htslib_bgzf_h) $(htslib_tbx_h) $(htslib_kseq_h) $(htslib_thread_pool_h) $(htslib_faidx_h) $(htslib_khash_str2int_h) $(bcftools_h) $(khash_str2str_h) tabix.o: tabix.c $(htslib_bgzf_h) $(htslib_tbx_h) ccall.o: ccall.c $(htslib_kfunc_h) $(call_h) kmin.h $(prob1_h) convert.o: convert.c $(htslib_vcf_h) $(htslib_synced_bcf_reader_h) $(htslib_vcfutils_h) $(bcftools_h) $(convert_h) convert.o: convert.c $(htslib_vcf_h) $(htslib_synced_bcf_reader_h) $(htslib_vcfutils_h) $(htslib_kfunc_h) $(bcftools_h) $(variantkey_h) $(convert_h) tsv2vcf.o: tsv2vcf.c $(tsv2vcf_h) em.o: em.c $(htslib_vcf_h) kmin.h $(call_h) filter.o: filter.c $(htslib_khash_str2int_h) $(htslib_hts_defs_h) $(htslib_vcfutils_h) $(htslib_kfunc_h) config.h $(filter_h) $(bcftools_h) $(CC) $(CFLAGS) $(ALL_CPPFLAGS) $(EXTRA_CPPFLAGS) $(PERL_CFLAGS) -c -o $@ $< gvcf.o: gvcf.c $(gvcf_h) $(bcftools_h) kmin.o: kmin.c kmin.h mcall.o: mcall.c $(htslib_kfunc_h) $(call_h) mcall.o: mcall.c $(htslib_kfunc_h) $(htslib_khash_str2int_h) $(call_h) prob1.o: prob1.c $(prob1_h) vcmp.o: vcmp.c $(htslib_hts_h) $(htslib_vcf_h) vcmp.h ploidy.o: ploidy.c $(htslib_khash_str2int_h) $(htslib_kseq_h) $(htslib_hts_h) $(bcftools_h) $(ploidy_h) polysomy.o: polysomy.c $(htslib_vcf_h) $(htslib_synced_bcf_reader_h) $(bcftools_h) peakfit.h peakfit.o: peakfit.c peakfit.h $(htslib_hts_h) $(htslib_kstring_h) bin.o: bin.c $(bcftools_h) bin.h cols.o: cols.c cols.h regidx.o: regidx.c $(htslib_hts_h) $(htslib_kstring_h) $(htslib_kseq_h) $(htslib_khash_str2int_h) regidx.h consensus.o: consensus.c $(htslib_vcf_h) $(htslib_kstring_h) $(htslib_synced_bcf_reader_h) $(htslib_kseq_h) $(htslib_bgzf_h) regidx.h $(bcftools_h) rbuf.h $(filter_h) mpileup.o: mpileup.c $(htslib_sam_h) $(htslib_faidx_h) $(htslib_kstring_h) $(htslib_khash_str2int_h) regidx.h $(bcftools_h) $(bam2bcf_h) $(bam_sample_h) $(gvcf_h) Loading @@ -242,25 +281,28 @@ csq.o: csq.c $(htslib_hts_h) $(htslib_vcf_h) $(htslib_synced_bcf_reader_h) $(hts # For tests that might use it, set $REF_PATH explicitly to use only reference # areas within the test suite (or set it to ':' to use no reference areas). # (regression.sh sets $REF_PATH to a subdirectory itself.) test-no-plugins: $(PROGRAMS) $(TEST_PROGRAMS) $(BGZIP) $(TABIX) # # If using MSYS, avoid poor shell expansion via: # MSYS2_ARG_CONV_EXCL="*" make check check test-no-plugins: $(PROGRAMS) $(TEST_PROGRAMS) $(BGZIP) $(TABIX) ./test/test-rbuf ./test/test-regidx REF_PATH=: ./test/test.pl --exec bgzip=$(BGZIP) --exec tabix=$(TABIX) REF_PATH=: ./test/test.pl --exec bgzip=$(BGZIP) --exec tabix=$(TABIX) --htsdir=$(HTSDIR) $${TEST_OPTS:-} test-plugins: $(PROGRAMS) $(TEST_PROGRAMS) $(BGZIP) $(TABIX) plugins check-plugins test-plugins: $(PROGRAMS) $(TEST_PROGRAMS) $(BGZIP) $(TABIX) plugins ./test/test-rbuf ./test/test-regidx REF_PATH=: ./test/test.pl --plugins --exec bgzip=$(BGZIP) --exec tabix=$(TABIX) REF_PATH=: ./test/test.pl --plugins --exec bgzip=$(BGZIP) --exec tabix=$(TABIX) --htsdir=$(HTSDIR) $${TEST_OPTS:-} test/test-rbuf.o: test/test-rbuf.c rbuf.h test/test-rbuf: test/test-rbuf.o $(CC) $(LDFLAGS) -o $@ $^ $(ALL_LIBS) test/test-regidx.o: test/test-regidx.c $(htslib_kstring_h) regidx.h test/test-regidx.o: test/test-regidx.c $(htslib_kstring_h) $(htslib_hts_os_h) regidx.h test/test-regidx: test/test-regidx.o regidx.o $(HTSLIB) $(CC) $(ALL_LDFLAGS) -o $@ $^ $(HTSLIB) -lpthread $(HTSLIB_LIB) $(ALL_LIBS) test/test-regidx: test/test-regidx.o regidx.o | $(HTSLIB) $(CC) $(ALL_LDFLAGS) -o $@ $^ $(HTSLIB_LIB) -lpthread $(ALL_LIBS) # make docs target depends the a2x asciidoc program Loading @@ -282,18 +324,19 @@ install: $(PROGRAMS) $(PLUGINS) $(INSTALL_PROGRAM) $(PROGRAMS) $(DESTDIR)$(bindir) $(INSTALL_SCRIPT) $(MISC_SCRIPTS) $(DESTDIR)$(misc_bindir) $(INSTALL_MAN) doc/bcftools.1 $(DESTDIR)$(man1dir) $(INSTALL_PROGRAM) plugins/*.so $(DESTDIR)$(plugindir) $(INSTALL_PROGRAM) plugins/*$(PLUGIN_EXT) $(DESTDIR)$(plugindir) clean: testclean clean-plugins -rm -f gmon.out *.o *~ $(PROGRAMS) version.h plugins/*.so plugins/*.P -rm -rf *.dSYM plugins/*.dSYM test/*.dSYM -rm -f gmon.out *.o *.a *~ $(PROGRAMS) version.h -rm -rf *.dSYM test/*.dSYM clean-plugins: -rm -f plugins/*.so plugins/*.P -rm -f plugins/*$(PLUGIN_EXT) plugins/*.P -rm -rf plugins/*.dSYM testclean: -rm -f test/*.o test/*~ $(TEST_PROGRAMS) -rm -f test/*.hex distclean: clean -rm -f config.cache config.h config.log config.mk config.status Loading NEWS +138 −13 Original line number Diff line number Diff line ## Release 1.10 (6th December 2019) * Numerous bug fixes, usability improvements and sanity checks were added to prevent common user errors. * The -r, --regions (and -R, --regions-file) option should never create unsorted VCFs or duplicates records again. This also fixes rare cases where a spanning deletion makes a subsequent record invisible to `bcftools isec` and other commands. * Additions to filtering and formatting expressions - support for the spanning deletion alternate allele (ALT=*) - new ILEN filtering expression to be able to filter by indel length - new MEAN, MEDIAN, MODE, STDEV, phred filtering functions - new formatting expression %PBINOM (phred-scaled binomial probability), %INFO (the whole INFO column), %FORMAT (the whole FORMAT column), %END (end position of the REF allele), %END0 (0-based end position of the REF allele), %MASK (with multiple files indicates the presence of the site in other files) * New plugins - `+gvcfz`: compress gVCF file by resizing gVCF blocks according to specified criteria - `+indel-stats`: collect various indel-specific statistics - `+parental-origin`: determine parental origin of a CNV region - `+remove-overlaps`: remove overlapping variants. - `+split-vep`: query structured annotations such INFO/CSQ created by bcftools/csq or VEP - `+trio-dnm`: screen variants for possible de-novo mutations in trios * `annotate` - new -l, --merge-logic option for combining multiple overlapping regions * `call` - new `bcftools call -G, --group-samples` option which allows grouping samples into populations and applying the HWE assumption within but not across the groups. * `csq` - significant reduction of memory usage in the local -l mode for VCFs with thousands of samples and 20% reduction in the non-local haplotype-aware mode. - fixes a small memory leak and formatting issue in FORMAT/BCSQ at sites with many consequences - do not print protein sequence of start_lost events - support for "start_retained" consequence - support for symbolic insertions (ALT="<INS...>"), "feature_elongation" consequence - new -b, --brief-predictions option to output abbreviated protein predictions. * `concat` - the `--naive` command now checks header compatibility when concatenating multiple files. * `consensus` - add a new `-H, --haplotype 1pIu/2pIu` feature to output first/second allele for phased genotypes and the IUPAC code for unphased genotypes - new -p, --prefix option to add a prefix to sequence names on output * `+contrast` - added support for Fisher's test probability and other annotations * `+fill-from-fasta` - new -N, --replace-non-ACGTN option * `+dosage` - fix some serious bugs in dosage calculation * `+fill-tags` - extended to perform simple on-the-fly calculations such as calculating INFO/DP from FORMAT/DP. * `merge` - add support for merging FORMAT strings - bug fixed in gVCF merging * `mpileup` - a new optional SCR annotation for the number of soft-clipped reads * `reheader` - new -f, --fai option for updating contig lines in the VCF header * `+trio-stats` - extend output to include DNM homs and recurrent DNMs * VariantKey support ## Release 1.9 (18th July 2018) * `annotate` Loading @@ -18,21 +139,22 @@ * `convert` - the --tsv2vcf option now makes the missing genotypes diploid, "./." instead of "." - the --tsv2vcf option now makes the missing genotypes diploid, "./." instead of "." - the behavior of -i/-e with --gvcf2vcf changed. Previously only sites with FILTER set to "PASS" or "." were expanded and the -i/-e options dropped sites completely. The new behavior is to let the -i/-e options control which records will be expanded. In order to drop records completely, one can stream through "bcftools view" first. sites completely. The new behavior is to let the -i/-e options control which records will be expanded. In order to drop records completely, one can stream through "bcftools view" first. * `csq` - since the real consequence of start/splice events are not known, the aminoacid positions at subsequent variants should stay unchanged - since the real consequence of start/splice events are not known, the amino acid positions at subsequent variants should stay unchanged - add `--force` option to skip malformatted transcripts in GFFs with out-of-phase CDS exons. - add `--force` option to skip malformatted transcripts in GFFs with out-of-phase CDS exons. * `+dosage`: output all alleles and all their dosages at multiallelic sites Loading @@ -52,25 +174,28 @@ - fix a parsing problem, '@' was not removed from '@filename' expressions * `mpileup`: fixed bug where, if samples were renamed using the `-G` (`--read-groups`) option, some samples could be omitted from the output file. * `mpileup`: fixed bug where, if samples were renamed using the `-G` (`--read-groups`) option, some samples could be omitted from the output file. * `norm`: update INFO/END when normalizing indels * `+split`: new -S option to subset samples and to use custom file names instead of the defaults * `+split`: new -S option to subset samples and to use custom file names instead of the defaults * `+smpl-stats`: new plugin * `+trio-stats`: new plugin * Fixed build problems with non-functional configure script produced on some platforms * Fixed build problems with non-functional configure script produced on some platforms ## Release 1.8 (April 2018) * `-i, -e` filtering: Support for custom perl scripts * `+contrast`: New plugin to annotate genotype differences between groups of samples * `+contrast`: New plugin to annotate genotype differences between groups of samples * `+fixploidy`: New options for simpler ploidy usage Loading bam2bcf.c +28 −5 File changed.Preview size limit exceeded, changes collapsed. Show changes Loading
.appveyor.yml 0 → 100644 +54 −0 Original line number Diff line number Diff line # version format. # you can use {branch} name in version format too # version: 1.0.{build}-{branch} version: 'vers.{build}' # branches to build branches: # Whitelist only: - develop # Blacklist except: - gh-pages # Do not build on tags (GitHub and BitBucket) skip_tags: true # Skipping commits affecting specific files (GitHub only). More details here: /docs/appveyor-yml #skip_commits: # files: # - docs/* # - '**/*.html' # We use Mingw/Msys, so use pacman for installs install: - set HOME=. - set MSYSTEM=MINGW64 - set PATH=C:/msys64/usr/bin;C:/msys64/mingw64/bin;%PATH% - set MINGWPREFIX=x86_64-w64-mingw32 - "sh -lc \"pacman -S --noconfirm --needed base-devel mingw-w64-x86_64-toolchain mingw-w64-x86_64-zlib mingw-w64-x86_64-bzip2 mingw-w64-x86_64-xz mingw-w64-x86_64-curl\"" # The user may have e.g. jkbonfield/bcftools branch FOO and an associated # jkbonfield/htslib branch FOO. If so use that related htslib, obtained by # munging $APPVEYOR_REPO_NAME. Otherwise we assume this is a PR only to # bcftools and should be linked against samtools(org)/htslib develop branch. clone_script: - "sh -lc \"if test x$APPVEYOR_PULL_REQUEST_HEAD_REPO_NAME != x ; then git clone --branch=$APPVEYOR_PULL_REQUEST_HEAD_REPO_BRANCH https://github.com/$APPVEYOR_PULL_REQUEST_HEAD_REPO_NAME $APPVEYOR_BUILD_FOLDER ; else false ; fi || git clone --branch=$APPVEYOR_REPO_BRANCH https://github.com/$APPVEYOR_REPO_NAME $APPVEYOR_BUILD_FOLDER\"" - "sh -lc \"git show-branch --sha1-name HEAD" - "sh -lc \"git clone --branch=$APPVEYOR_REPO_BRANCH https://github.com/`echo $APPVEYOR_REPO_NAME|sed 's#/bcftools#/htslib#'`.git $APPVEYOR_BUILD_FOLDER/htslib || git clone https://github.com/samtools/htslib.git $APPVEYOR_BUILD_FOLDER/htslib \"" - "sh -lc \"cd $APPVEYOR_BUILD_FOLDER/htslib && git show-branch --sha1-name HEAD\"" build_script: - set HOME=. - set MSYSTEM=MINGW64 - set PATH=C:/msys64/usr/bin;C:/msys64/mingw64/bin;%PATH% - "sh -lc \"(cd htslib; aclocal && autoheader && autoconf)\"" - "sh -lc \"aclocal && autoheader && autoconf && ./configure && make -j2\"" test_script: - set HOME=. - set MSYSTEM=MINGW64 - set PATH=C:/msys64/usr/bin;C:/msys64/mingw64/bin;%APPVEYOR_BUILD_FOLDER%/htslib;%PATH% - "sh -lc \"MSYS2_ARG_CONV_EXCL=* make test-plugins\""
LICENSE +23 −0 Original line number Diff line number Diff line Loading @@ -723,3 +723,26 @@ Public License instead of this License. But first, please read ----------------------------------------------------------------------------- LICENSE FOR VariantKey (https://github.com/Genomicsplc/variantkey) The MIT License Copyright (c) 2017-2018 GENOMICS plc Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
Makefile +73 −30 Original line number Diff line number Diff line Loading @@ -23,8 +23,10 @@ # DEALINGS IN THE SOFTWARE. CC = gcc AR = ar RANLIB = ranlib CPPFLAGS = CFLAGS = -g -Wall -Wc++-compat -O2 CFLAGS = -g -Wall -O2 LDFLAGS = LIBS = Loading @@ -36,11 +38,12 @@ OBJS = main.o vcfindex.o tabix.o \ vcfstats.o vcfisec.o vcfmerge.o vcfquery.o vcffilter.o filter.o vcfsom.o \ vcfnorm.o vcfgtcheck.o vcfview.o vcfannotate.o vcfroh.o vcfconcat.o \ vcfcall.o mcall.o vcmp.o gvcf.o reheader.o convert.o vcfconvert.o tsv2vcf.o \ vcfcnv.o HMM.o vcfplugin.o consensus.o ploidy.o bin.o hclust.o version.o \ vcfcnv.o HMM.o consensus.o ploidy.o bin.o hclust.o version.o \ regidx.o smpl_ilist.o csq.o vcfbuf.o \ mpileup.o bam2bcf.o bam2bcf_indel.o bam_sample.o \ vcfsort.o \ vcfsort.o cols.o \ ccall.o em.o prob1.o kmin.o # the original samtools calling PLUGIN_OBJS = vcfplugin.o prefix = /usr/local exec_prefix = $(prefix) Loading Loading @@ -73,11 +76,18 @@ MISC_SCRIPTS = \ misc/vcfutils.pl TEST_PROGRAMS = test/test-rbuf test/test-regidx all: $(PROGRAMS) $(TEST_PROGRAMS) plugins ALL_CPPFLAGS = -I. $(HTSLIB_CPPFLAGS) $(CPPFLAGS) ALL_LDFLAGS = $(HTSLIB_LDFLAGS) $(LDFLAGS) ALL_LIBS = -lz -ldl $(LIBS) ALL_LIBS = -lz $(DL_LIBS) $(LIBS) all: $(PROGRAMS) $(TEST_PROGRAMS) plugins EXTRA_CPPFLAGS = GSL_LIBS = # On windows, plugins need to be fully linked. This adds the extra libraries # needed. Defined here so config.mk can override it. W32_PLUGIN_LIBS = libbcftools.a $(HTSLIB_DLL) $(ALL_LIBS) # Usually config.mk and config.h are generated by running configure # or config.status, but if those aren't used create defaults here. Loading @@ -88,12 +98,12 @@ config.h: echo '/* Basic config.h generated by Makefile */' > $@ ifneq "$(PLUGINS_ENABLED)" "no" echo '#define ENABLE_BCF_PLUGINS 1' >> $@ echo '#define PLUGIN_EXT ".so"' >> $@ echo '#define PLUGIN_EXT "$(PLUGIN_EXT)"' >> $@ endif include config.mk PACKAGE_VERSION = 1.9 PACKAGE_VERSION = 1.10 # If building from a Git repository, replace $(PACKAGE_VERSION) with the Git # description of the working tree: either a release tag with the same value Loading Loading @@ -134,14 +144,15 @@ ifdef USE_GPL GSL_LIBS ?= -lgsl -lcblas endif bcftools: $(OBJS) $(HTSLIB) $(CC) $(DYNAMIC_FLAGS) -pthread $(ALL_LDFLAGS) -o $@ $(OBJS) $(HTSLIB_LIB) -lm $(ALL_LIBS) $(GSL_LIBS) $(PERL_LIBS) print-%: @echo '$*=$($*)' # Plugin rules ifneq "$(PLUGINS_ENABLED)" "no" PLUGINC = $(foreach dir, plugins, $(wildcard $(dir)/*.c)) PLUGINS = $(PLUGINC:.c=$(PLUGIN_EXT)) PLUGINM = $(PLUGINC:.c=.mk) OBJS += $(PLUGIN_OBJS) ifneq "$(origin PLATFORM)" "file" PLATFORM := $(shell uname -s) Loading @@ -149,12 +160,35 @@ endif ifeq "$(PLATFORM)" "Darwin" $(PLUGINS): | bcftools PLUGIN_FLAGS = -bundle -bundle_loader bcftools -Wl,-undefined,dynamic_lookup DL_LIBS = else ifeq "$(PLATFORM)" "CYGWIN" $(PLUGINS): | bcftools PLUGIN_FLAGS = -fPIC -shared PLUGIN_LIBS = $(W32_PLUGIN_LIBS) DL_LIBS = -ldl else ifneq "$(filter MINGW% MSYS%,$(PLATFORM))" "" DYNAMIC_FLAGS = $(PLUGINS): | bcftools PLUGIN_FLAGS = -fPIC -shared -Wl,-export-all-symbols PLUGIN_LIBS = $(W32_PLUGIN_LIBS) # On windows, plugins need to be fully linked, including bcftools_version() symbol # from the application they will be loaded into. DL_LIBS = else PLUGIN_FLAGS = -fPIC -shared DL_LIBS = -ldl endif libbcftools.a: $(OBJS) @-rm -f $@ $(AR) -rc $@ $(OBJS) -$(RANLIB) $@ vcfplugin.o: EXTRA_CPPFLAGS += -DPLUGINPATH='"$(pluginpath)"' %.dll %.cygdll: %.c version.h version.c libbcftools.a $(HTSLIB_DLL) $(CC) $(PLUGIN_FLAGS) $(CFLAGS) $(ALL_CPPFLAGS) $(EXTRA_CPPFLAGS) $(LDFLAGS) -o $@ version.c $< $(PLUGIN_LIBS) %.so: %.c version.h version.c $(CC) $(PLUGIN_FLAGS) $(CFLAGS) $(ALL_CPPFLAGS) $(EXTRA_CPPFLAGS) $(LDFLAGS) -o $@ version.c $< $(LIBS) Loading @@ -172,10 +206,14 @@ test check: test-no-plugins endif # PLUGINS_ENABLED bcftools: $(OBJS) $(HTSLIB) $(CC) $(DYNAMIC_FLAGS) -pthread $(ALL_LDFLAGS) -o $@ $(OBJS) $(HTSLIB_LIB) -lm $(ALL_LIBS) $(GSL_LIBS) $(PERL_LIBS) plugins: $(PLUGINS) bcftools_h = bcftools.h $(htslib_hts_defs_h) $(htslib_vcf_h) call_h = call.h $(htslib_vcf_h) $(htslib_synced_bcf_reader_h) vcmp.h variantkey_h = variantkey.h hex.h convert_h = convert.h $(htslib_vcf_h) tsv2vcf_h = tsv2vcf.h $(htslib_vcf_h) filter_h = filter.h $(htslib_vcf_h) Loading @@ -189,41 +227,42 @@ bam2bcf_h = bam2bcf.h $(htslib_hts_h) $(htslib_vcf_h) bam_sample_h = bam_sample.h $(htslib_sam_h) main.o: main.c $(htslib_hts_h) config.h version.h $(bcftools_h) vcfannotate.o: vcfannotate.c $(htslib_vcf_h) $(htslib_synced_bcf_reader_h) $(htslib_kseq_h) $(htslib_khash_str2int_h) $(bcftools_h) vcmp.h $(filter_h) $(convert_h) $(smpl_ilist_h) $(htslib_khash_h) vcfannotate.o: vcfannotate.c $(htslib_vcf_h) $(htslib_synced_bcf_reader_h) $(htslib_kseq_h) $(htslib_khash_str2int_h) $(bcftools_h) vcmp.h $(filter_h) $(convert_h) $(smpl_ilist_h) regidx.h $(htslib_khash_h) vcfplugin.o: vcfplugin.c config.h $(htslib_vcf_h) $(htslib_synced_bcf_reader_h) $(htslib_kseq_h) $(htslib_khash_str2int_h) $(bcftools_h) vcmp.h $(filter_h) vcfcall.o: vcfcall.c $(htslib_vcf_h) $(htslib_kfunc_h) $(htslib_synced_bcf_reader_h) $(htslib_khash_str2int_h) $(bcftools_h) $(call_h) $(prob1_h) $(ploidy_h) $(gvcf_h) vcfconcat.o: vcfconcat.c $(htslib_vcf_h) $(htslib_synced_bcf_reader_h) $(htslib_kseq_h) $(htslib_bgzf_h) $(htslib_tbx_h) $(bcftools_h) vcfcall.o: vcfcall.c $(htslib_vcf_h) $(htslib_kfunc_h) $(htslib_synced_bcf_reader_h) $(htslib_khash_str2int_h) $(bcftools_h) $(call_h) $(prob1_h) $(ploidy_h) $(gvcf_h) regidx.h $(vcfbuf_h) vcfconcat.o: vcfconcat.c $(htslib_vcf_h) $(htslib_synced_bcf_reader_h) $(htslib_kseq_h) $(htslib_bgzf_h) $(htslib_tbx_h) $(htslib_thread_pool_h) $(bcftools_h) vcfconvert.o: vcfconvert.c $(htslib_faidx_h) $(htslib_vcf_h) $(htslib_bgzf_h) $(htslib_synced_bcf_reader_h) $(htslib_vcfutils_h) $(htslib_kseq_h) $(bcftools_h) $(filter_h) $(convert_h) $(tsv2vcf_h) vcffilter.o: vcffilter.c $(htslib_vcf_h) $(htslib_synced_bcf_reader_h) $(htslib_vcfutils_h) $(bcftools_h) $(filter_h) rbuf.h vcfgtcheck.o: vcfgtcheck.c $(htslib_vcf_h) $(htslib_synced_bcf_reader_h) $(htslib_vcfutils_h) $(bcftools_h) hclust.h vcfindex.o: vcfindex.c $(htslib_vcf_h) $(htslib_tbx_h) $(htslib_kstring_h) $(htslib_bgzf_h) $(bcftools_h) vcfisec.o: vcfisec.c $(htslib_vcf_h) $(htslib_synced_bcf_reader_h) $(htslib_vcfutils_h) $(bcftools_h) $(filter_h) vcfisec.o: vcfisec.c $(htslib_vcf_h) $(htslib_synced_bcf_reader_h) $(htslib_vcfutils_h) $(htslib_hts_os_h) $(bcftools_h) $(filter_h) vcfmerge.o: vcfmerge.c $(htslib_vcf_h) $(htslib_synced_bcf_reader_h) $(htslib_vcfutils_h) $(htslib_faidx_h) regidx.h $(bcftools_h) vcmp.h $(htslib_khash_h) vcfnorm.o: vcfnorm.c $(htslib_vcf_h) $(htslib_synced_bcf_reader_h) $(htslib_faidx_h) $(htslib_khash_str2int_h) $(bcftools_h) rbuf.h vcfquery.o: vcfquery.c $(htslib_vcf_h) $(htslib_synced_bcf_reader_h) $(htslib_khash_str2int_h) $(htslib_vcfutils_h) $(bcftools_h) $(filter_h) $(convert_h) vcfroh.o: vcfroh.c $(htslib_vcf_h) $(htslib_synced_bcf_reader_h) $(htslib_kstring_h) $(htslib_kseq_h) $(htslib_bgzf_h) $(bcftools_h) HMM.h $(smpl_ilist_h) $(filter_h) vcfcnv.o: vcfcnv.c $(htslib_vcf_h) $(htslib_synced_bcf_reader_h) $(htslib_kstring_h) $(htslib_kfunc_h) $(htslib_khash_str2int_h) $(bcftools_h) HMM.h rbuf.h vcfsom.o: vcfsom.c $(htslib_vcf_h) $(htslib_synced_bcf_reader_h) $(htslib_vcfutils_h) $(bcftools_h) vcfsort.o: vcfsort.c $(htslib_vcf_h) $(htslib_kstring_h) kheap.h $(bcftools_h) vcfsom.o: vcfsom.c $(htslib_vcf_h) $(htslib_synced_bcf_reader_h) $(htslib_vcfutils_h) $(htslib_hts_os_h) $(bcftools_h) vcfsort.o: vcfsort.c $(htslib_vcf_h) $(htslib_kstring_h) $(htslib_hts_os_h) kheap.h $(bcftools_h) vcfstats.o: vcfstats.c $(htslib_vcf_h) $(htslib_synced_bcf_reader_h) $(htslib_vcfutils_h) $(htslib_faidx_h) $(bcftools_h) $(filter_h) bin.h vcfview.o: vcfview.c $(htslib_vcf_h) $(htslib_synced_bcf_reader_h) $(htslib_vcfutils_h) $(bcftools_h) $(filter_h) $(htslib_khash_str2int_h) reheader.o: reheader.c $(htslib_vcf_h) $(htslib_bgzf_h) $(htslib_tbx_h) $(htslib_kseq_h) $(htslib_thread_pool_h) $(bcftools_h) $(khash_str2str_h) reheader.o: reheader.c $(htslib_vcf_h) $(htslib_bgzf_h) $(htslib_tbx_h) $(htslib_kseq_h) $(htslib_thread_pool_h) $(htslib_faidx_h) $(htslib_khash_str2int_h) $(bcftools_h) $(khash_str2str_h) tabix.o: tabix.c $(htslib_bgzf_h) $(htslib_tbx_h) ccall.o: ccall.c $(htslib_kfunc_h) $(call_h) kmin.h $(prob1_h) convert.o: convert.c $(htslib_vcf_h) $(htslib_synced_bcf_reader_h) $(htslib_vcfutils_h) $(bcftools_h) $(convert_h) convert.o: convert.c $(htslib_vcf_h) $(htslib_synced_bcf_reader_h) $(htslib_vcfutils_h) $(htslib_kfunc_h) $(bcftools_h) $(variantkey_h) $(convert_h) tsv2vcf.o: tsv2vcf.c $(tsv2vcf_h) em.o: em.c $(htslib_vcf_h) kmin.h $(call_h) filter.o: filter.c $(htslib_khash_str2int_h) $(htslib_hts_defs_h) $(htslib_vcfutils_h) $(htslib_kfunc_h) config.h $(filter_h) $(bcftools_h) $(CC) $(CFLAGS) $(ALL_CPPFLAGS) $(EXTRA_CPPFLAGS) $(PERL_CFLAGS) -c -o $@ $< gvcf.o: gvcf.c $(gvcf_h) $(bcftools_h) kmin.o: kmin.c kmin.h mcall.o: mcall.c $(htslib_kfunc_h) $(call_h) mcall.o: mcall.c $(htslib_kfunc_h) $(htslib_khash_str2int_h) $(call_h) prob1.o: prob1.c $(prob1_h) vcmp.o: vcmp.c $(htslib_hts_h) $(htslib_vcf_h) vcmp.h ploidy.o: ploidy.c $(htslib_khash_str2int_h) $(htslib_kseq_h) $(htslib_hts_h) $(bcftools_h) $(ploidy_h) polysomy.o: polysomy.c $(htslib_vcf_h) $(htslib_synced_bcf_reader_h) $(bcftools_h) peakfit.h peakfit.o: peakfit.c peakfit.h $(htslib_hts_h) $(htslib_kstring_h) bin.o: bin.c $(bcftools_h) bin.h cols.o: cols.c cols.h regidx.o: regidx.c $(htslib_hts_h) $(htslib_kstring_h) $(htslib_kseq_h) $(htslib_khash_str2int_h) regidx.h consensus.o: consensus.c $(htslib_vcf_h) $(htslib_kstring_h) $(htslib_synced_bcf_reader_h) $(htslib_kseq_h) $(htslib_bgzf_h) regidx.h $(bcftools_h) rbuf.h $(filter_h) mpileup.o: mpileup.c $(htslib_sam_h) $(htslib_faidx_h) $(htslib_kstring_h) $(htslib_khash_str2int_h) regidx.h $(bcftools_h) $(bam2bcf_h) $(bam_sample_h) $(gvcf_h) Loading @@ -242,25 +281,28 @@ csq.o: csq.c $(htslib_hts_h) $(htslib_vcf_h) $(htslib_synced_bcf_reader_h) $(hts # For tests that might use it, set $REF_PATH explicitly to use only reference # areas within the test suite (or set it to ':' to use no reference areas). # (regression.sh sets $REF_PATH to a subdirectory itself.) test-no-plugins: $(PROGRAMS) $(TEST_PROGRAMS) $(BGZIP) $(TABIX) # # If using MSYS, avoid poor shell expansion via: # MSYS2_ARG_CONV_EXCL="*" make check check test-no-plugins: $(PROGRAMS) $(TEST_PROGRAMS) $(BGZIP) $(TABIX) ./test/test-rbuf ./test/test-regidx REF_PATH=: ./test/test.pl --exec bgzip=$(BGZIP) --exec tabix=$(TABIX) REF_PATH=: ./test/test.pl --exec bgzip=$(BGZIP) --exec tabix=$(TABIX) --htsdir=$(HTSDIR) $${TEST_OPTS:-} test-plugins: $(PROGRAMS) $(TEST_PROGRAMS) $(BGZIP) $(TABIX) plugins check-plugins test-plugins: $(PROGRAMS) $(TEST_PROGRAMS) $(BGZIP) $(TABIX) plugins ./test/test-rbuf ./test/test-regidx REF_PATH=: ./test/test.pl --plugins --exec bgzip=$(BGZIP) --exec tabix=$(TABIX) REF_PATH=: ./test/test.pl --plugins --exec bgzip=$(BGZIP) --exec tabix=$(TABIX) --htsdir=$(HTSDIR) $${TEST_OPTS:-} test/test-rbuf.o: test/test-rbuf.c rbuf.h test/test-rbuf: test/test-rbuf.o $(CC) $(LDFLAGS) -o $@ $^ $(ALL_LIBS) test/test-regidx.o: test/test-regidx.c $(htslib_kstring_h) regidx.h test/test-regidx.o: test/test-regidx.c $(htslib_kstring_h) $(htslib_hts_os_h) regidx.h test/test-regidx: test/test-regidx.o regidx.o $(HTSLIB) $(CC) $(ALL_LDFLAGS) -o $@ $^ $(HTSLIB) -lpthread $(HTSLIB_LIB) $(ALL_LIBS) test/test-regidx: test/test-regidx.o regidx.o | $(HTSLIB) $(CC) $(ALL_LDFLAGS) -o $@ $^ $(HTSLIB_LIB) -lpthread $(ALL_LIBS) # make docs target depends the a2x asciidoc program Loading @@ -282,18 +324,19 @@ install: $(PROGRAMS) $(PLUGINS) $(INSTALL_PROGRAM) $(PROGRAMS) $(DESTDIR)$(bindir) $(INSTALL_SCRIPT) $(MISC_SCRIPTS) $(DESTDIR)$(misc_bindir) $(INSTALL_MAN) doc/bcftools.1 $(DESTDIR)$(man1dir) $(INSTALL_PROGRAM) plugins/*.so $(DESTDIR)$(plugindir) $(INSTALL_PROGRAM) plugins/*$(PLUGIN_EXT) $(DESTDIR)$(plugindir) clean: testclean clean-plugins -rm -f gmon.out *.o *~ $(PROGRAMS) version.h plugins/*.so plugins/*.P -rm -rf *.dSYM plugins/*.dSYM test/*.dSYM -rm -f gmon.out *.o *.a *~ $(PROGRAMS) version.h -rm -rf *.dSYM test/*.dSYM clean-plugins: -rm -f plugins/*.so plugins/*.P -rm -f plugins/*$(PLUGIN_EXT) plugins/*.P -rm -rf plugins/*.dSYM testclean: -rm -f test/*.o test/*~ $(TEST_PROGRAMS) -rm -f test/*.hex distclean: clean -rm -f config.cache config.h config.log config.mk config.status Loading
NEWS +138 −13 Original line number Diff line number Diff line ## Release 1.10 (6th December 2019) * Numerous bug fixes, usability improvements and sanity checks were added to prevent common user errors. * The -r, --regions (and -R, --regions-file) option should never create unsorted VCFs or duplicates records again. This also fixes rare cases where a spanning deletion makes a subsequent record invisible to `bcftools isec` and other commands. * Additions to filtering and formatting expressions - support for the spanning deletion alternate allele (ALT=*) - new ILEN filtering expression to be able to filter by indel length - new MEAN, MEDIAN, MODE, STDEV, phred filtering functions - new formatting expression %PBINOM (phred-scaled binomial probability), %INFO (the whole INFO column), %FORMAT (the whole FORMAT column), %END (end position of the REF allele), %END0 (0-based end position of the REF allele), %MASK (with multiple files indicates the presence of the site in other files) * New plugins - `+gvcfz`: compress gVCF file by resizing gVCF blocks according to specified criteria - `+indel-stats`: collect various indel-specific statistics - `+parental-origin`: determine parental origin of a CNV region - `+remove-overlaps`: remove overlapping variants. - `+split-vep`: query structured annotations such INFO/CSQ created by bcftools/csq or VEP - `+trio-dnm`: screen variants for possible de-novo mutations in trios * `annotate` - new -l, --merge-logic option for combining multiple overlapping regions * `call` - new `bcftools call -G, --group-samples` option which allows grouping samples into populations and applying the HWE assumption within but not across the groups. * `csq` - significant reduction of memory usage in the local -l mode for VCFs with thousands of samples and 20% reduction in the non-local haplotype-aware mode. - fixes a small memory leak and formatting issue in FORMAT/BCSQ at sites with many consequences - do not print protein sequence of start_lost events - support for "start_retained" consequence - support for symbolic insertions (ALT="<INS...>"), "feature_elongation" consequence - new -b, --brief-predictions option to output abbreviated protein predictions. * `concat` - the `--naive` command now checks header compatibility when concatenating multiple files. * `consensus` - add a new `-H, --haplotype 1pIu/2pIu` feature to output first/second allele for phased genotypes and the IUPAC code for unphased genotypes - new -p, --prefix option to add a prefix to sequence names on output * `+contrast` - added support for Fisher's test probability and other annotations * `+fill-from-fasta` - new -N, --replace-non-ACGTN option * `+dosage` - fix some serious bugs in dosage calculation * `+fill-tags` - extended to perform simple on-the-fly calculations such as calculating INFO/DP from FORMAT/DP. * `merge` - add support for merging FORMAT strings - bug fixed in gVCF merging * `mpileup` - a new optional SCR annotation for the number of soft-clipped reads * `reheader` - new -f, --fai option for updating contig lines in the VCF header * `+trio-stats` - extend output to include DNM homs and recurrent DNMs * VariantKey support ## Release 1.9 (18th July 2018) * `annotate` Loading @@ -18,21 +139,22 @@ * `convert` - the --tsv2vcf option now makes the missing genotypes diploid, "./." instead of "." - the --tsv2vcf option now makes the missing genotypes diploid, "./." instead of "." - the behavior of -i/-e with --gvcf2vcf changed. Previously only sites with FILTER set to "PASS" or "." were expanded and the -i/-e options dropped sites completely. The new behavior is to let the -i/-e options control which records will be expanded. In order to drop records completely, one can stream through "bcftools view" first. sites completely. The new behavior is to let the -i/-e options control which records will be expanded. In order to drop records completely, one can stream through "bcftools view" first. * `csq` - since the real consequence of start/splice events are not known, the aminoacid positions at subsequent variants should stay unchanged - since the real consequence of start/splice events are not known, the amino acid positions at subsequent variants should stay unchanged - add `--force` option to skip malformatted transcripts in GFFs with out-of-phase CDS exons. - add `--force` option to skip malformatted transcripts in GFFs with out-of-phase CDS exons. * `+dosage`: output all alleles and all their dosages at multiallelic sites Loading @@ -52,25 +174,28 @@ - fix a parsing problem, '@' was not removed from '@filename' expressions * `mpileup`: fixed bug where, if samples were renamed using the `-G` (`--read-groups`) option, some samples could be omitted from the output file. * `mpileup`: fixed bug where, if samples were renamed using the `-G` (`--read-groups`) option, some samples could be omitted from the output file. * `norm`: update INFO/END when normalizing indels * `+split`: new -S option to subset samples and to use custom file names instead of the defaults * `+split`: new -S option to subset samples and to use custom file names instead of the defaults * `+smpl-stats`: new plugin * `+trio-stats`: new plugin * Fixed build problems with non-functional configure script produced on some platforms * Fixed build problems with non-functional configure script produced on some platforms ## Release 1.8 (April 2018) * `-i, -e` filtering: Support for custom perl scripts * `+contrast`: New plugin to annotate genotype differences between groups of samples * `+contrast`: New plugin to annotate genotype differences between groups of samples * `+fixploidy`: New options for simpler ploidy usage Loading
