Fix a consensus bug

which prevented reading fasta files containing empty lines

Resolves #2424

Author: pd3

NEWS

@@ -1,8 +1,18 @@
 ## Release a.b
 
 
+Changes affecting the whole of bcftools, or multiple commands:
+
+* The `-i/-e` filtering expressions and `-f` formatting in `query`
+
+    - Add a new function `smpl_COUNT()/sCOUNT()` which returns the number of elements (#2423)
+
 Changes affecting specific commands:
 
+* bcftools consensus
+
+    - Fix a bug which prevented reading fasta files containing empty lines in their entirety (#2424)
+
 * bcftools gtcheck
 
     - The program is now able to process gVCF blocks. Newly, monoallelic sites are excluded only

consensus.c

@@ -1093,7 +1093,7 @@ static void consensus(args_t *args)
     BGZF *fasta = bgzf_open(args->ref_fname, "r");
     if ( !fasta ) error("Error reading %s\n", args->ref_fname);
     kstring_t str = {0,0,0};
-    while ( bgzf_getline(fasta, '\n', &str) > 0 )
+    while ( bgzf_getline(fasta, '\n', &str) >= 0 )
     {
         if ( str.s[0]=='>' )
         {

test/consensus.overlaps.2.fa

@@ -0,0 +1,5 @@
+>1
+CGGGACAC
+
+>2
+CGGGACAC

test/test.pl

@@ -940,6 +940,7 @@
 run_test(\&test_vcf_convert_tsv2vcf,$opts,in=>'convert.23andme',out=>'convert.23andme.vcf',args=>'-c ID,CHROM,POS,AA -s SAMPLE1',fai=>'23andme');
 run_test(\&test_vcf_convert_tsv2vcf,$opts,in=>'convert.tsv',out=>'convert.tsv.vcf',args=>'-c -,CHROM,POS,REF,ALT',fai=>'23andme');
 run_test(\&test_vcf_consensus,$opts,in=>'consensus.gvcf-missing.1',out=>'consensus.gvcf-missing.1.out',fa=>'consensus.gvcf-missing.fa',args=>'--missing N');
+run_test(\&test_vcf_consensus,$opts,in=>'consensus.overlaps.1',out=>'consensus.overlaps.1.1.out',fa=>'consensus.overlaps.2.fa',args=>'-s A');
 run_test(\&test_vcf_consensus,$opts,in=>'consensus.overlaps.1',out=>'consensus.overlaps.1.1.out',fa=>'consensus.overlaps.1.fa',args=>'-s A');
 run_test(\&test_vcf_consensus,$opts,in=>'consensus.overlaps.1',out=>'consensus.overlaps.1.2.out',fa=>'consensus.overlaps.1.fa',args=>'-s B');
 run_test(\&test_vcf_consensus,$opts,in=>'consensus.overlaps.1',out=>'consensus.overlaps.1.3.out',fa=>'consensus.overlaps.1.fa',args=>'-s A -a N');