Release 1.10

.appveyor.yml

@@ -0,0 +1,54 @@
+# 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\""

.gitignore

@@ -1,9 +1,13 @@
 bcftools
 *.o
+*.a
+*.exe
 /version.h
 plugins/*.so
 plugins/*.dSYM
 plugins/*.P
+plugins/*.dll
+plugins/*.cygdll
 
 aclocal.m4
 autom4te.cache
@@ -19,3 +23,7 @@ configure
 /test/test-regidx
 
 /TAGS
+
+test/vkrs.unsorted.hex
+test/rsvk.unsorted.hex
+test/nrvk.unsorted.tsv

.travis.yml

@@ -24,6 +24,11 @@ matrix:
     - os: osx
       compiler: clang
       env: USE_CONFIG=yes
+    # An optimised build with address, leak and undefined behavior checking
+    - os: linux
+      compiler: clang
+      sudo: required
+      env: CFLAGS="-fsanitize=address" LDFLAGS="-fsanitize=address" USE_CONFIG=yes
 
 env:
   global:
@@ -39,13 +44,26 @@ addons:
 
 # For MacOSX systems
 before_install:
-  - if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then brew update    ; fi
-  - if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then brew install xz gsl ; fi
+  - |
+    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
   # repository $HTSREPO setting) and check out a corresponding branch with the
   # same name, if any, or otherwise the default branch.
   - .travis/clone ${HTSREPO:-git://github.com/samtools/htslib.git} $HTSDIR $TRAVIS_BRANCH
 
-script: if test "$USE_CONFIG" = "yes" ; then ( cd "$HTSDIR" && autoreconf ) && autoreconf && ./configure --enable-libgsl && make && make test ; else make plugindir=$TRAVIS_BUILD_DIR/plugins -e && make -e test-plugins ; fi
+script: |
+  if test "$USE_CONFIG" = "yes"; then
+    ( cd "$HTSDIR" && autoreconf ) && \
+    autoreconf && \
+    ./configure --enable-libgsl && \
+    make && \
+    make test
+  else
+    make plugindir=$TRAVIS_BUILD_DIR/plugins -e && \
+    make -e test-plugins
+  fi

LICENSE

@@ -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

@@ -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     =
 
@@ -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)
@@ -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.
@@ -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
@@ -134,27 +144,51 @@ 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 := $(shell uname -s)
 endif
 ifeq "$(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)
 
@@ -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)
@@ -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)
@@ -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
@@ -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