Release 1.11

.travis.yml

@@ -45,10 +45,11 @@ addons:
 # For MacOSX systems
 before_install:
   - |
-    if [ "$TRAVIS_OS_NAME" == "osx" ]; then
-      brew update && \
-      brew install xz gsl
-    fi
+    # Removing GSL dependant parts as they are not tested anyway
+    # if [ "$TRAVIS_OS_NAME" == "osx" ]; then
+    #   brew update && \
+    #   brew install xz gsl
+    # fi
 
 before_script:
   # Clone samtools/htslib (or another repository, as specified by a Travis CI
@@ -60,7 +61,7 @@ script: |
   if test "$USE_CONFIG" = "yes"; then
     ( cd "$HTSDIR" && autoreconf ) && \
     autoreconf && \
-    ./configure --enable-libgsl && \
+    ./configure && \
     make && \
     make test
   else

INSTALL

@@ -1,3 +1,31 @@
+For the impatient
+=================
+
+The latest source code can be downloaded from github and compiled using:
+
+    git clone git://github.com/samtools/htslib.git
+    git clone git://github.com/samtools/bcftools.git
+    cd bcftools
+     # The following is optional:
+     #   autoheader && autoconf && ./configure --enable-libgsl --enable-perl-filters
+    make
+
+
+    IMPORTANT:
+    ---
+    In order to use the BCFtools plugins, this environment variable must be set and point
+    to the correct location
+
+        export BCFTOOLS_PLUGINS=/path/to/bcftools/plugins
+
+    ---
+
+Note that if also the polysomy command or support for Perl filtering should be included,
+the compilation instructions differ, see Optional Compilation with GSL and Optional
+Compilation with Perl below.
+
+
+
 System Requirements
 ===================
 
@@ -20,9 +48,9 @@ BCFtools and HTSlib depend on the following libraries:
                (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 the "System Specific Details" below for guidance on how to install
-these on a variety of systems.
+note that MacOS and some Linux distributions package these separately from the
+library 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.
@@ -61,7 +89,7 @@ If you have a full GNU autotools install, you can alternatively run:
     autoreconf
 
 Warnings like "AC_CONFIG_SUBDIRS: you should use literals" can be ignored
-or supressed using 'autoconf -Wno-syntax'.
+or suppressed using 'autoconf -Wno-syntax'.
 
 
 Compilation
@@ -72,12 +100,14 @@ Compilation
     ./configure
     make
 
-This BCFtools release contains a copy of HTSlib which will be used to build
-BCFtools.  If you already have a system-installed HTSlib or another HTSlib
-that you would prefer to build against, you can arrange this by using the
-configure script's --with-htslib option.  Use --with-htslib=DIR to point
-to an HTSlib source tree or installation in DIR; or --with-htslib=system
-to use a system-installed HTSlib.
+If installing from a tarballs (as opposed form github), BCFtools release
+contains a copy of HTSlib which will be used to build BCFtools. If you
+already have a system-installed HTSlib or another HTSlib that you would
+prefer to build against, you can arrange this by using the configure script's
+--with-htslib option. Use --with-htslib=DIR to point to an HTSlib source tree
+or installation in DIR; or --with-htslib=system to use a system-installed HTSlib.
+When downloaded from github and --with-htslib option is not given, the directory
+../htslib is used.
 
 
 Optional Compilation with Perl
@@ -89,6 +119,16 @@ 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
+
+Note that when compiling on MacOS, the default options for linking with Perl
+provided by the system sometimes do not work. It was reported that removing
+the occurrence of -arch i386 from config.mk solved the problem.
+
+
 Optional Compilation with GSL
 =============================
 
@@ -136,6 +176,7 @@ 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
 =======================
 
@@ -166,10 +207,21 @@ sudo yum install autoconf automake make gcc perl-Data-Dumper zlib-devel bzip2 bz
 Alpine Linux
 ------------
 
+Note: To install gsl-dev, it may be necessary to enable the "community"
+repository in /etc/apk/repositories.
+
 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
+
+
+MacOS, assuming Xcode is installed:
+-----
+xz
+gsl (optional)
+
+

Makefile

@@ -41,7 +41,7 @@ OBJS     = main.o vcfindex.o tabix.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 cols.o \
+           vcfsort.o cols.o extsort.o \
            ccall.o em.o prob1.o kmin.o # the original samtools calling
 PLUGIN_OBJS = vcfplugin.o
 
@@ -69,6 +69,7 @@ INSTALL_SCRIPT  = $(INSTALL_PROGRAM)
 PROGRAMS = bcftools
 MISC_SCRIPTS = \
     misc/color-chrs.pl \
+    misc/gff2gff.py \
     misc/guess-ploidy.py \
     misc/plot-vcfstats \
     misc/plot-roh.py \
@@ -103,7 +104,7 @@ endif
 
 include config.mk
 
-PACKAGE_VERSION = 1.10.2
+PACKAGE_VERSION = 1.11
 
 # 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
@@ -136,7 +137,7 @@ print-version:
 	$(CC) $(CFLAGS) $(ALL_CPPFLAGS) $(EXTRA_CPPFLAGS) -c -o $@ $<
 
 # The polysomy command is not compiled by default because it brings dependency
-# on libgsl. The command can be compiled wth `make USE_GPL=1`. See the INSTALL
+# on libgsl. The command can be compiled with `make USE_GPL=1`. See the INSTALL
 # and LICENSE documents to understand license implications.
 ifdef USE_GPL
     main.o : EXTRA_CPPFLAGS += -DUSE_GPL
@@ -176,8 +177,13 @@ PLUGIN_LIBS = $(W32_PLUGIN_LIBS)
 DL_LIBS =
 else
 PLUGIN_FLAGS = -fPIC -shared
+ifeq "$(PLATFORM)" "default"
+# Configure was used and has already added -ldl to $(LIBS) if necessary
+DL_LIBS =
+else
 DL_LIBS = -ldl
 endif
+endif
 
 libbcftools.a: $(OBJS)
 	@-rm -f $@
@@ -207,7 +213,7 @@ 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)
+	$(CC) $(DYNAMIC_FLAGS) $(ALL_LDFLAGS) -o $@ $(OBJS) $(HTSLIB_LIB) -lm $(ALL_LIBS) $(GSL_LIBS) $(PERL_LIBS) -lpthread
 
 plugins: $(PLUGINS)
 
@@ -233,7 +239,7 @@ vcfcall.o: vcfcall.c $(htslib_vcf_h) $(htslib_kfunc_h) $(htslib_synced_bcf_reade
 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
+vcfgtcheck.o: vcfgtcheck.c $(htslib_vcf_h) $(htslib_synced_bcf_reader_h) $(htslib_vcfutils_h) $(htslib_kbitset_h) $(bcftools_h) extsort.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) $(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)
@@ -248,7 +254,7 @@ vcfview.o: vcfview.c $(htslib_vcf_h) $(htslib_synced_bcf_reader_h) $(htslib_vcfu
 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) $(htslib_kfunc_h) $(bcftools_h) $(variantkey_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) $(filter_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)
@@ -273,6 +279,7 @@ version.o: version.h version.c
 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
+extsort.o: extsort.c $(bcftools_h) extsort.h kheap.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