Update Appveyor script.

Fix Windows paths inside quoted arguments.

.appveyor.yml

@@ -28,15 +28,17 @@ install:
   - 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 mingw-w64-x86_64-dlfcn\""
+  - "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 $APPVEYOR_REPO_NAME.  Otherwise we assume this is a PR only to
 # bcftools and should be linked against samtools(org)/htslib develop branch.
 clone_script:
-  - "sh -lc \"git clone --branch=$APPVEYOR_REPO_BRANCH https://github.com/$APPVEYOR_REPO_NAME $APPVEYOR_BUILD_FOLDER\""
+  - "sh -lc \"if test x$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=.
@@ -49,4 +51,5 @@ test_script:
   - set HOME=.
   - set MSYSTEM=MINGW64
   - set PATH=C:/msys64/usr/bin;C:/msys64/mingw64/bin;%PATH%
+  - set BCFTOOLS_PLUGINS=./plugins
   - "sh -lc \"MSYS2_ARG_CONV_EXCL=* make test-plugins\""

Makefile

@@ -170,7 +170,6 @@ PLUGIN_FLAGS = -fPIC -shared -Wl,-export-all-symbols
 PLUGIN_LIBS = libbcftools.a $(HTSLIB_DLL) $(ALL_LIBS)
 # On windows, plugins need to be fully linked, including bcftools_version() symbol
 # from the application they will be loaded into.
-BCFTOOLS_IMPLIB = -Wl,-out-implib,libbcftools.a
 else
 PLUGIN_FLAGS = -fPIC -shared
 endif
@@ -182,7 +181,7 @@ libbcftools.a: $(OBJS)
 
 vcfplugin.o: EXTRA_CPPFLAGS += -DPLUGINPATH='"$(pluginpath)"'
 
-%.dll: %.c version.h version.c libbcftools.a
+%.dll: %.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)
@@ -328,7 +327,7 @@ clean: testclean clean-plugins
 	-rm -rf *.dSYM plugins/*.dSYM test/*.dSYM
 
 clean-plugins:
-	-rm -f plugins/*.so plugins/*.P
+	-rm -f plugins/*.so plugins/*.P plugins/*.dll
 	-rm -rf plugins/*.dSYM
 
 testclean:

filter.c

@@ -2013,15 +2013,15 @@ static void parse_tag_idx(bcf_hdr_t *hdr, int is_fmt, char *tag, char *tag_idx,
     int *idxs2 = NULL, nidxs2 = 0, idx2 = 0;
 
     int set_samples = 0;
-#ifdef _WIN32
-    char *colon = strrchr(tag_idx, ';');
-#else
     char *colon = strrchr(tag_idx, ':');
-#endif
     if ( tag_idx[0]=='@' )     // file list with sample names
     {
         if ( !is_fmt ) error("Could not parse \"%s\". (Not a FORMAT tag yet a sample list provided.)\n", ori);
         char *fname = expand_path(tag_idx+1);
+#ifdef _WIN32
+        if (fname && strlen(fname) > 2 && fname[1] == ':') // Deal with Windows paths, such as 'C:\..'
+            colon = strrchr(fname+2, ':');
+#endif
         int nsmpl;
         char **list = hts_readlist(fname, 1, &nsmpl);
         if ( !list && colon )
@@ -2030,11 +2030,7 @@ static void parse_tag_idx(bcf_hdr_t *hdr, int is_fmt, char *tag, char *tag_idx,
             tok->idxs  = idxs2;
             tok->nidxs = nidxs2;
             tok->idx   = idx2;
-#ifdef _WIN32
-            colon = strrchr(fname, ';');
-#else
             colon = strrchr(fname, ':');
-#endif
             *colon = 0;
             list = hts_readlist(fname, 1, &nsmpl);
         }

test/test.pl

@@ -307,8 +307,8 @@
 test_vcf_plugin($opts,in=>'plugin1',out=>'missing2ref.out',cmd=>'+missing2ref --no-version');
 test_vcf_plugin($opts,in=>'plugin1',out=>'missing2ref.out',cmd=>'+setGT --no-version',args=>'-- -t . -n 0');
 test_vcf_plugin($opts,in=>'setGT',out=>'setGT.1.out',cmd=>'+setGT --no-version',args=>'-- -t q -n 0 -i \'GT~"." && FMT/DP=30 && GQ=150\'');
-test_vcf_plugin($opts,in=>'setGT.2',out=>'setGT.2.out',cmd=>'+setGT --no-version',args=>'-- -t q -n . -i \'GT[@{PATH}/setGT.samples.txt]="het"\'');
-test_vcf_plugin($opts,in=>'setGT.2',out=>'setGT.3.out',cmd=>'+setGT --no-version',args=>'-- -t q -n . -i \'GT[@{PATH}/setGT.samples.txt]="het" & binom(AD[@{PATH}/setGT.samples.txt])<0.1\'');
+test_vcf_plugin($opts,in=>'setGT.2',out=>'setGT.2.out',cmd=>'+setGT --no-version',args=>'-- -t q -n . -i \'GT[@{QPATH}/setGT.samples.txt]="het"\'');
+test_vcf_plugin($opts,in=>'setGT.2',out=>'setGT.3.out',cmd=>'+setGT --no-version',args=>'-- -t q -n . -i \'GT[@{QPATH}/setGT.samples.txt]="het" & binom(AD[@{QPATH}/setGT.samples.txt])<0.1\'');
 test_vcf_annotate($opts,in=>'annotate9',tab=>'annots9',out=>'annotate9.out',args=>'-c CHROM,POS,REF,ALT,+ID');
 test_vcf_plugin($opts,in=>'plugin1',out=>'fill-AN-AC.out',cmd=>'+fill-AN-AC --no-version');
 test_vcf_plugin($opts,in=>'dosage',out=>'dosage.1.out',cmd=>'+dosage',args=>'-- -t PL');
@@ -505,8 +505,8 @@ sub parse_params
     $$opts{bin}  = $FindBin::RealBin;
     $$opts{bin}  =~ s{/test/?$}{};
     if ($^O =~ /^msys/) {
-	$$opts{path} = cygpath($$opts{path});
-	$$opts{bin}  = cygpath($$opts{bin});
+        $$opts{path} = cygpath($$opts{path});
+        $$opts{bin}  = cygpath($$opts{bin});
     }
     
     return $opts;
@@ -1043,6 +1043,12 @@ sub test_vcf_plugin
     if ( !$$opts{test_plugins} ) { return; }
     $ENV{BCFTOOLS_PLUGINS} = "$$opts{bin}/plugins";
     if ( !exists($args{args}) ) { $args{args} = ''; }
+    my $wpath = $$opts{path}; 
+    if ($^O =~ /^msys/) {
+        $wpath = `cygpath -w $$opts{path}`;
+        $wpath =~ s/\r?\n//;
+    }
+    $args{args} =~ s/{QPATH}/$wpath/g;
     $args{args} =~ s/{PATH}/$$opts{path}/g;
     $args{cmd}  =~ s/{PATH}/$$opts{path}/g;
     $args{args} =~ s/{TMP}/$$opts{tmp}/g;