Commit 99b97632 authored by Andreas Tille's avatar Andreas Tille
Browse files

New upstream version 1.9

parent 27af1f68

INSTALL

+60 −23
Original line number Diff line number Diff line 
System Requirements

===================



BCFtools and HTSlib depend on the zlib library <http://zlib.net>, the bzip2

library <http://bzip.org/> and liblzma <http://tukaani.org/xz/>.  Building

them requires development files to be installed on the build machine;

BCFtools and HTSlib depend on the following libraries:



  BCFtools:

    zlib       <http://zlib.net>

    gsl        <https://www.gnu.org/software/gsl/>

               (optional, for the 'polysomy' command)

    libperl    <http://www.perl.org/>

               (optional, to support filters using perl syntax)



  HTSlib:

    zlib       <http://zlib.net>

    libbz2     <http://bzip.org/>

    liblzma    <http://tukaani.org/xz/>

    libcurl    <https://curl.haxx.se/>

               (optional but strongly recommended, for network access)

    libcrypto  <https://www.openssl.org/>

               (optional, for Amazon S3 support; not needed on MacOS)



Building them requires development files to be installed on the build machine;

note that some Linux distributions package these separately from the library

itself (see below).

itself.  See the "System Specific Details" below for guidance on how to install

these on a variety of systems.



The bzip2 and liblzma dependencies can be removed if full CRAM support

is not needed - see HTSlib's INSTALL file for details.



Packages for dpkg-based Linux distributions (Debian / Ubuntu) are:



  zlib1g-dev

  libbz2-dev

  liblzma-dev



Packages for rpm or yum-based Linux distributions (RedHat / Fedora / CentOS)

are:



  zlib-devel

  bzip2-devel

  xz-devel



To build BCFtools, you will need:



    GNU make
@@ -85,12 +89,6 @@ sophisticated filtering. This option can be enabled by supplying the 


    ./configure --enable-perl-filters



Note that enabling this option changes the license from MIT to GPL

because bcftools need to be built with



    perl -MExtUtils::Embed -e ccopts -e ldopts





Optional Compilation with GSL

=============================
@@ -136,3 +134,42 @@ The bgzip and tabix utilities are provided by HTSlib. If you have not also 
installed HTSlib separately, you may wish to install these utilities by hand

by copying bcftools-1.x/htslib-1.x/{bgzip,tabix} to the same bin directory

to which you have installed bcftools et al.





System Specific Details

=======================



Installing the prerequisites is system dependent and there is more

than one correct way of satisfying these, including downloading them

from source, compiling and installing them yourself.



For people with super-user access, we provide an example set of commands

below for installing the dependencies on a variety of operating system

distributions.  Note these are not specific recommendations on distribution,

compiler or SSL implementation.  It is assumed you already have the core set

of packages for the given distribution - the lists may be incomplete if

this is not the case.



Debian / Ubuntu

---------------



sudo apt-get update  # Ensure the package list is up to date

sudo apt-get install autoconf automake make gcc perl zlib1g-dev libbz2-dev liblzma-dev libcurl4-gnutls-dev libssl-dev libperl-dev libgsl0-dev



Note: libcurl4-openssl-dev can be used as an alternative to libcurl4-gnutls-dev.



RedHat / CentOS

---------------



sudo yum install autoconf automake make gcc perl-Data-Dumper zlib-devel bzip2 bzip2-devel xz-devel curl-devel openssl-devel gsl-devel perl-ExtUtils-Embed



Alpine Linux

------------



sudo apk update  # Ensure the package list is up to date

sudo apk add autoconf automake make gcc musl-dev perl bash zlib-dev bzip2-dev xz-dev curl-dev libressl-dev gsl-dev perl-dev



OpenSUSE

--------



sudo zypper install autoconf automake make gcc perl zlib-devel libbz2-devel xz-devel libcurl-devel libopenssl-devel gsl-devel

Makefile

+34 −30
Original line number Diff line number Diff line
@@ -93,7 +93,7 @@ endif 


include config.mk



PACKAGE_VERSION = 1.8

PACKAGE_VERSION = 1.9



# 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
@@ -175,63 +175,67 @@ endif # PLUGINS_ENABLED 
plugins: $(PLUGINS)



bcftools_h = bcftools.h $(htslib_hts_defs_h) $(htslib_vcf_h)

bin_h = bin.h $(htslib_hts_h)

call_h = call.h $(htslib_vcf_h) $(htslib_synced_bcf_reader_h) vcmp.h

convert_h = convert.h $(htslib_vcf_h)

tsv2vcf_h = tsv2vcf.h $(htslib_vcf_h)

filter_h = filter.h $(htslib_vcf_h)

gvcf_h = gvcf.h $(bcftools_h)

khash_str2str_h = khash_str2str.h $(htslib_khash_h)

ploidy_h = ploidy.h regidx.h

prob1_h = prob1.h $(htslib_vcf_h) $(call_h)

roh_h = HMM.h $(htslib_vcf_h) $(htslib_synced_bcf_reader_h) $(htslib_kstring_h) $(htslib_kseq_h) $(bcftools_h)

cnv_h = HMM.h $(htslib_vcf_h) $(htslib_synced_bcf_reader_h)

smpl_ilist_h = smpl_ilist.h $(htslib_vcf_h)

vcfbuf_h = vcfbuf.h $(htslib_vcf_h)

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) $(bcftools_h) vcmp.h $(filter_h)

vcfplugin.o: vcfplugin.c config.h $(htslib_vcf_h) $(htslib_synced_bcf_reader_h) $(htslib_kseq_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)

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)

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)

vcfconvert.o: vcfconvert.c $(htslib_vcf_h) $(htslib_bgzf_h) $(htslib_synced_bcf_reader_h) $(htslib_vcfutils_h) $(bcftools_h) $(filter_h) $(convert_h) $(tsv2vcf_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)

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)

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) $(bcftools_h) rbuf.h

vcfquery.o: vcfquery.c $(htslib_vcf_h) $(htslib_synced_bcf_reader_h) $(htslib_vcfutils_h) $(bcftools_h) $(filter_h) $(convert_h)

vcfroh.o: vcfroh.c $(roh_h)

vcfcnv.o: vcfcnv.c $(cnv_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) $(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)

reheader.o: reheader.c $(htslib_vcf_h) $(htslib_bgzf_h) $(htslib_tbx_h) $(htslib_kseq_h) $(bcftools_h)

vcfsort.o: vcfsort.c $(htslib_vcf_h) $(htslib_kstring_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)

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)

tsv2vcf.o: tsv2vcf.c $(tsv2vcf_h)

em.o: em.c $(htslib_vcf_h) kmin.h $(call_h)

filter.o: filter.c config.h $(htslib_khash_str2int_h) $(filter_h) $(bcftools_h) $(htslib_hts_defs_h) $(htslib_vcfutils_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 $(call_h)

gvcf.o: gvcf.c $(gvcf_h) $(bcftools_h)

kmin.o: kmin.c kmin.h

mcall.o: mcall.c $(htslib_kfunc_h) $(call_h)

prob1.o: prob1.c $(prob1_h)

vcmp.o: vcmp.c $(htslib_hts_h) vcmp.h

ploidy.o: ploidy.c regidx.h $(htslib_khash_str2int_h) $(htslib_kseq_h) $(htslib_hts_h) $(bcftools_h) $(ploidy_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 $(bin_h)

bin.o: bin.c $(bcftools_h) bin.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_hts_h) $(htslib_kseq_h) rbuf.h $(bcftools_h) regidx.h

mpileup.o: mpileup.c $(htslib_sam_h) $(htslib_faidx_h) $(htslib_kstring_h) $(htslib_khash_str2int_h) regidx.h $(bcftools_h) $(call_h) $(bam2bcf_h) $(bam_sample_h)

bam_sample.o: $(bam_sample_h) $(htslib_hts_h) $(htslib_khash_str2int_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)

bam2bcf.o: bam2bcf.c $(htslib_hts_h) $(htslib_sam_h) $(htslib_kstring_h) $(htslib_kfunc_h) $(bam2bcf_h) mw.h

bam2bcf_indel.o: bam2bcf_indel.c $(htslib_hts_h) $(htslib_sam_h) $(htslib_khash_str2int_h) $(bam2bcf_h) $(htslib_ksort_h)

bam_sample.o: bam_sample.c $(htslib_hts_h) $(htslib_kstring_h) $(htslib_khash_str2int_h) $(khash_str2str_h) $(bam_sample_h) $(bcftools_h)

version.o: version.h version.c

hclust.o: hclust.c hclust.h

vcfbuf.o: vcfbuf.c vcfbuf.h rbuf.h

smpl_ilist.o: smpl_ilist.c smpl_ilist.h

csq.o: csq.c smpl_ilist.h regidx.h filter.h kheap.h rbuf.h

hclust.o: hclust.c $(htslib_hts_h) $(htslib_kstring_h) $(bcftools_h) hclust.h

HMM.o: HMM.c $(htslib_hts_h) HMM.h

vcfbuf.o: vcfbuf.c $(htslib_vcf_h) $(htslib_vcfutils_h) $(bcftools_h) $(vcfbuf_h) rbuf.h

smpl_ilist.o: smpl_ilist.c $(bcftools_h) $(smpl_ilist_h)

csq.o: csq.c $(htslib_hts_h) $(htslib_vcf_h) $(htslib_synced_bcf_reader_h) $(htslib_khash_h) $(htslib_khash_str2int_h) $(htslib_kseq_h) $(htslib_faidx_h) $(bcftools_h) $(filter_h) regidx.h kheap.h $(smpl_ilist_h) rbuf.h



# test programs
@@ -253,7 +257,7 @@ 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 regidx.h

test/test-regidx.o: test/test-regidx.c $(htslib_kstring_h) regidx.h



test/test-regidx: test/test-regidx.o regidx.o $(HTSLIB)

	$(CC) $(ALL_LDFLAGS) -o $@ $^ $(HTSLIB) -lpthread $(HTSLIB_LIB) $(ALL_LIBS)

NEWS

+68 −0
Original line number Diff line number Diff line 
## Release 1.9 (18th July 2018)



* `annotate`



    - REF and ALT columns can be now transferred from the annotation file.



    - fixed bug when setting vector_end values.



* `consensus`



    - new -M option to control output at missing genotypes



    - variants immediately following insersions should not be skipped.  Note

      however, that the current fix requires normalized VCF and may still

      falsely skip variants adjacent to multiallelic indels.



    - bug fixed in -H selection handling



* `convert`



    - 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.



* `csq`



    - since the real consequence of start/splice events are not known, the aminoacid

      positions at subsequent variants should stay unchanged



    - 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



* `+fixref`: fix serious bug in -m top conversion



* `-i/-e` filtering expressions:



    - add two-tailed binomial test



    - add functions N_PASS() and F_PASS()



    - add support for lists of samples in filtering expressions, with many

      samples it was impractical to list them all on the command line. Samples

      can be now in a file as, e.g., GT[@samples.txt]="het"



    - allow multiple perl functions in the expressions and some bug fixes



    - 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.



* `norm`: update INFO/END when normalizing indels



* `+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





## Release 1.8 (April 2018)



* `-i, -e` filtering: Support for custom perl scripts

bam_sample.c

+9 −4
Original line number Diff line number Diff line 
/*  bam_sample.c -- group data by sample.



    Copyright (C) 2010, 2011 Broad Institute.

    Copyright (C) 2013, 2016 Genome Research Ltd.

    Copyright (C) 2013, 2016-2018 Genome Research Ltd.



    Author: Heng Li <lh3@sanger.ac.uk>, Petr Danecek <pd3@sanger.ac.uk>
@@ -167,10 +167,14 @@ int bam_smpl_add_bam(bam_smpl_t *bsmpl, char *bam_hdr, const char *fname) 
    void *bam_smpls = khash_str2int_init();

    int first_smpl = -1, nskipped = 0;

    const char *p = bam_hdr, *q, *r;

    while ((q = strstr(p, "@RG")) != 0) 

    while (p != NULL && (q = strstr(p, "@RG")) != 0)

    {

        char *eol = strchr(q + 3, '\n');

        if (q > bam_hdr && *(q - 1) != '\n') { // @RG must be at start of line

            p = eol;

            continue;

        }

        p = q + 3;

        r = q = 0;

        if ((q = strstr(p, "\tID:")) != 0) q += 4;

        if ((r = strstr(p, "\tSM:")) != 0) r += 4;

        if (r && q)
@@ -220,7 +224,7 @@ int bam_smpl_add_bam(bam_smpl_t *bsmpl, char *bam_hdr, const char *fname) 
        }

        else

            break;

        p = q > r ? q : r;

        p = eol;

    }

    int nsmpls = khash_str2int_size(bam_smpls);

    khash_str2int_destroy_free(bam_smpls);
@@ -234,6 +238,7 @@ int bam_smpl_add_bam(bam_smpl_t *bsmpl, char *bam_hdr, const char *fname) 
    {

        // no suitable read group is available in this bam: ignore the whole file.

        free(file->fname);

        if ( file->rg2idx ) khash_str2int_destroy_free(file->rg2idx);

        bsmpl->nfiles--;

        return -1;

    }

bcftools.h

+1 −1
Original line number Diff line number Diff line
@@ -39,7 +39,7 @@ THE SOFTWARE. */ 
#define FT_STDIN (1<<3)



char *bcftools_version(void);

void error(const char *format, ...) HTS_NORETURN;

void error(const char *format, ...) HTS_NORETURN HTS_FORMAT(HTS_PRINTF_FMT, 1, 2);

void bcf_hdr_append_version(bcf_hdr_t *hdr, int argc, char **argv, const char *cmd);

const char *hts_bcf_wmode(int file_type);