Resolve test.pl merge conflict

Author: pd3

LICENSE

@@ -723,11 +723,12 @@ Public License instead of this License.  But first, please read
 
 -----------------------------------------------------------------------------
 
-LICENSE FOR VariantKey (https://github.com/Genomicsplc/variantkey)
+LICENSE FOR VariantKey (https://github.com/tecnickcom/variantkey)
 
 The MIT License
 
 Copyright (c) 2017-2018 GENOMICS plc
+Copyright (c) 2018-2023 Nicola Asuni - Tecnick.com
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal

Makefile

@@ -42,7 +42,7 @@ OBJS     = main.o vcfindex.o tabix.o \
            regidx.o smpl_ilist.o csq.o vcfbuf.o \
            mpileup.o bam2bcf.o bam2bcf_indel.o bam2bcf_iaux.o read_consensus.o bam_sample.o \
            vcfsort.o cols.o extsort.o dist.o abuf.o \
-           ccall.o em.o prob1.o kmin.o str_finder.o
+           ccall.o em.o prob1.o kmin.o str_finder.o gff.o
 PLUGIN_OBJS = vcfplugin.o
 
 prefix      = /usr/local
@@ -246,7 +246,7 @@ vcfgtcheck.o: vcfgtcheck.c $(htslib_vcf_h) $(htslib_synced_bcf_reader_h) $(htsli
 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)
-vcfnorm.o: vcfnorm.c $(htslib_vcf_h) $(htslib_synced_bcf_reader_h) $(htslib_faidx_h) $(htslib_khash_str2int_h) $(bcftools_h) rbuf.h abuf.h
+vcfnorm.o: vcfnorm.c $(htslib_vcf_h) $(htslib_synced_bcf_reader_h) $(htslib_faidx_h) $(htslib_khash_str2int_h) $(bcftools_h) rbuf.h abuf.h gff.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) $(smpl_ilist_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
@@ -289,6 +289,7 @@ vcfbuf.o: vcfbuf.c $(htslib_vcf_h) $(htslib_vcfutils_h) $(htslib_hts_os_h) $(bcf
 abuf.o: abuf.c $(htslib_vcf_h) $(bcftools_h) rbuf.h abuf.h
 extsort.o: extsort.c $(bcftools_h) extsort.h kheap.h
 smpl_ilist.o: smpl_ilist.c $(bcftools_h) $(smpl_ilist_h)
+gff.o: gff.c gff.h regidx.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

NEWS

@@ -14,6 +14,8 @@ Changes affecting specific commands:
 
     - Fix a bug where the `-m` function did not respect the `--min-overlap` option (#1869)
 
+    - Fix a bug when update of INFO/END results in assertion error (#1957)
+
 * bcftools concat
 
     - New option `--drop-genotypes`
@@ -78,12 +80,19 @@ Changes affecting specific commands:
 
     - Symbolic <DEL.*> alleles are now normalized too (#1919)
 
+    - New `-g, --gff-annot` option to right-align indels in forward transcripts to follow
+      HGVS 3'rule (#1929)
+
 * bcftools query
 
     - Force newline character in formatting expression when not given explicitly
 
     - Fix `-H` header output in formatting expressions containing newlines
 
+* bcftools reheader
+
+    - Make `-f, --fai` aware of long contigs not representable by 32-bit integer (#1959)
+
 * bcftools +split-vep
 
     - Prevent a segfault when `-i/-e` use a VEP subfield not included in `-f` or `-c` (#1877)

consensus.c

@@ -324,7 +324,7 @@ static void init_region(args_t *args, char *line)
 {
     char *ss, *se = line;
     while ( *se && !isspace(*se) && *se!=':' ) se++;
-    int from = 0, to = 0;
+    hts_pos_t from = 0, to = 0;
     char tmp = 0, *tmp_ptr = NULL;
     if ( *se )
     {
@@ -356,7 +356,14 @@ static void init_region(args_t *args, char *line)
     args->fa_frz_mod = -1;
     args->fa_case    = -1;
     args->vcf_rbuf.n = 0;
-    bcf_sr_seek(args->files,line,args->fa_ori_pos);
+
+    kstring_t str = {0,0,0};
+    if ( from==0 ) from = 1;
+    if ( to==0 ) to = HTS_POS_MAX;
+    ksprintf(&str,"%s:%"PRIhts_pos"-%"PRIhts_pos,line,from,to);
+    bcf_sr_set_regions(args->files,line,0);
+    free(str.s);
+
     if ( tmp_ptr ) *tmp_ptr = tmp;
     fprintf(args->fp_out,">%s%s\n",args->chr_prefix?args->chr_prefix:"",line);
     if ( args->chain_fname )