New -H, --header-line option

This is a convenience option that allows to pass a header line on command line,
and complements the existing `-h, --header-lines` option which requires a file
with header lines

Author: pd3

Makefile

@@ -230,12 +230,13 @@ prob1_h = prob1.h $(htslib_vcf_h) $(call_h)
 smpl_ilist_h = smpl_ilist.h $(htslib_vcf_h)
 vcfbuf_h = vcfbuf.h $(htslib_vcf_h)
 abuf_h = abuf.h $(htslib_vcf_h)
+dbuf_h = dbuf.h $(htslib_vcf_h)
 bam2bcf_h = bam2bcf.h $(htslib_hts_h) $(htslib_vcf_h)
 bam_sample_h = bam_sample.h $(htslib_sam_h)
 
 str_finder.o: str_finder.h utlist.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) regidx.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) $(dbuf_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) 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)

dbuf.h

@@ -0,0 +1,71 @@
+/* The MIT License
+
+   Copyright (c) 2022 Genome Research Ltd.
+
+   Author: Petr Danecek <pd3@sanger.ac.uk>
+
+   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.
+
+ */
+
+/*
+    Simple data buffer
+*/
+
+#ifndef __DBUF_H__
+#define __DBUF_H__
+
+#include <htslib/hts.h>
+
+typedef struct
+{
+    size_t n,m;
+    void **dat;
+}
+dbuf_t;
+
+static inline dbuf_t *dbuf_push(dbuf_t *buf, void *ptr)
+{
+    if ( !buf ) buf = calloc(1,sizeof(dbuf_t));
+    buf->n++;
+    hts_expand(void*,buf->n,buf->m,buf->dat);
+    buf->dat[buf->n-1] = ptr;
+    return buf;
+}
+
+static inline void *dbuf_ith(dbuf_t *buf, int i)
+{
+    return buf->dat[i];
+}
+
+static inline size_t dbuf_n(dbuf_t *buf)
+{
+    return buf->n;
+}
+
+static inline void dbuf_destroy_free(dbuf_t *buf)
+{
+    int i;
+    for (i=0; i<buf->n; i++) free(buf->dat[i]);
+    free(buf->dat);
+    free(buf);
+}
+
+#endif
+

test/test.pl

@@ -448,6 +448,7 @@
 test_vcf_annotate($opts,in=>'annotate14',out=>'annotate25.out',args=>'-x FILTER/XX,INFO/XX --force');
 test_vcf_annotate($opts,in=>'annotate15',tab=>'annotate15',out=>'annotate26.out',args=>'-s SAMPLE1 -c CHROM,FROM,TO,FMT/FOO,BAR');
 test_vcf_annotate($opts,in=>'annotate15',tab=>'annotate15',out=>'annotate27.out',args=>'-s SAMPLE2 -c CHROM,FROM,TO,FMT/FOO,BAR');
+test_vcf_annotate($opts,in=>'annotate15',tab=>'annotate15',out=>'annotate27.out',args=>q[-s SAMPLE2 -c CHROM,FROM,TO,FMT/FOO,BAR -H '##FORMAT=<ID=FOO,Number=1,Type=String,Description="Some description">' -H '##INFO=<ID=BAR,Number=1,Type=Integer,Description="Some description">']);
 test_vcf_annotate($opts,in=>'annotate16',out=>'annotate28.out',args=>'-x FILTER');
 test_vcf_annotate($opts,in=>'annotate17.1',tab=>'annotate17.1',out=>'annotate17.1.out',args=>'-c CHROM,BEG,END,A,B -l A:append,B:append');
 test_vcf_annotate($opts,in=>'annotate17.2',tab=>'annotate17.1',out=>'annotate17.2.out',args=>'-c CHROM,BEG,END,A,B -l A:append,B:append');
@@ -1514,7 +1515,7 @@ sub test_vcf_annotate
         bgzip_tabix($opts,file=>$args{tab},suffix=>'tab',args=>'-s1 -b2 -e2');
         $annot_fname = "-a $$opts{tmp}/$args{tab}.tab.gz";
         $in_fname = "$$opts{path}/$args{in}.vcf";
-        $hdr = -e "$$opts{path}/$args{in}.hdr" ? "-h $$opts{path}/$args{in}.hdr" : '';
+        $hdr = (-e "$$opts{path}/$args{in}.hdr" && !($args{args}=~/-H/) && !($args{args}=~/--header-line\s/)) ? "-h $$opts{path}/$args{in}.hdr" : '';
     }
     elsif ( exists($args{vcf}) )
     {