/*
* Writes an annotation list to disk. If reading is a negative number then
* it is assumed to be a contig number instead.
*
* Comp, start, end and length refer to the parameters for the reading that
* this tag is from.
*
* Offset should contain the offset of this reading in the contig when writing
* consensus tags.
*/
static void write_anno_list(GapIO *io, anno_info *ap, int len, int reading,
int offset, int comp, int start, int end,
int length) {
int i, start2, end2;
for (i = 0; i < len; i++) {
/*
* Clip to used length of sequence when translating tags to the
* consensus.
*/
if (reading < 0) {
if (comp) {
start2 = length - ap[i].end + 1;
end2 = length - ap[i].start + 1;
} else {
start2 = ap[i].start;
end2 = ap[i].end;
}
if (start2 + offset < 0)
start2 = 0 - offset;
/* Can't check yet as we don't know the contig length */
#if 0
if (end2 >= end)
end2 = end-1;
if (end2 < start2)
continue;
#endif
} else {
start2 = ap[i].start;
end2 = ap[i].end;
if (start2 + offset < 1 || end2 + offset > length) {
verror(ERR_WARN, "enter_reading",
"Tag on reading %s overlaps gel reading ends - not "
"entered", get_read_name(io, reading));
continue;
} else if (end2 < start2) {
verror(ERR_WARN, "enter_reading",
"Tag on reading %s has negative length - not entered",
get_read_name(io, reading));
continue;
}
}
insert_NEW_tag(io, (tag_id)reading, start2 + offset, end2 - start2 + 1,
ap[i].type, ap[i].comment, ap[i].strand);
}
return;
}
void bam_parser(opt_t *opt) {
samFile *in = sam_open(opt->in_name, "r");
if(in == NULL) die("bam_parser: fail to open file '%s'", opt->in_name);
// if output file exists but not force to overwrite
if(access(opt->out_name, F_OK)!=-1 && opt->f==false) die("bam_parser: %s exists, use opetion -f to overwrite", opt->out_name);
bam_hdr_t *header = sam_hdr_read(in);
bam1_t *aln = bam_init1();
int8_t *p;
int32_t n;
int ret;
while((ret=sam_read1(in, header, aln)) >= 0)
printf("name=%s\nflag=%d\nseq=%s\nqual=%s\nlane_id=%d\n", get_read_name(aln), aln->core.flag, get_sequence(aln), get_qualities(aln), get_lane_id(aln));
bam_destroy1(aln);
sam_close(in);
}
