[Samtools-devel] Add INFO lines to bcf_hdr_t; add INFO field to bcf_1_t

[Gregory B. <g.b...@im...>]

I’m writing a Mac app using the htslib C API, and I’m trying to work out how to add INFO lines to a bcf_hdr_t and then INFO fields to bcf_1_t records.

I can add INFO lines to the header using, eg.:
NSString *iLine = [NSString stringWithFormat:@"##INFO=<ID=UMME1,Number=1,Type=Integer,Description=\"UMassME1Hotspot;danRer7\",Source=\"http://hgdownload.soe.ucsc.edu/goldenPath/danRer7/database/UMassME1Hotspot.txt.gz\">"];
bcf_hdr_append(hdr, infoLine.UTF8String);

And the header seems to be OK, eg.
kstring_t htxt = {0,0,0};
if (bcf_hdr_format(hdr, 1, &htxt) == 0) {
    return [NSString stringWithUTF8String:htxt.s];
}

returns a string with the new INFO lines added (albeit after all of the contig lines).

But when I try to add an INFO field to a bcf_1_t record:
const char *key_c = “UMME1”;
int32_t val_i = 1;
bcf_update_info_int32(hdr, rec, key_c, &val_i, 1);

it crashes at line 3267 in vcf.c (bcf_update_info()):
if ( !bcf_hdr_idinfo_exists(hdr,BCF_HL_INFO,inf_id) ) return -1;

If I add an INFO field for one of the pre-existing INFO lines, it succeeds.

Any help would be appreciated.

Greg.