#include <stdio.h>
#include <ctype.h>
+#include <errno.h>
#include <assert.h>
#include "bam.h"
#include "bam_endian.h"
* CIGAR related routines *
**************************/
-int bam_segreg(int32_t pos, const bam1_core_t *c, const uint32_t *cigar, bam_segreg_t *reg)
-{
- unsigned k;
- int32_t x = c->pos, y = 0;
- int state = 0;
- for (k = 0; k < c->n_cigar; ++k) {
- int op = cigar[k] & BAM_CIGAR_MASK; // operation
- int l = cigar[k] >> BAM_CIGAR_SHIFT; // length
- if (state == 0 && (op == BAM_CMATCH || op == BAM_CDEL || op == BAM_CINS) && x + l > pos) {
- reg->tbeg = x; reg->qbeg = y; reg->cbeg = k;
- state = 1;
- }
- if (op == BAM_CMATCH) { x += l; y += l; }
- else if (op == BAM_CDEL || op == BAM_CREF_SKIP) x += l;
- else if (op == BAM_CINS || op == BAM_CSOFT_CLIP) y += l;
- if (state == 1 && (op == BAM_CSOFT_CLIP || op == BAM_CHARD_CLIP || op == BAM_CREF_SKIP || k == c->n_cigar - 1)) {
- reg->tend = x; reg->qend = y; reg->cend = k;
- }
- }
- return state? 0 : -1;
-}
-
uint32_t bam_calend(const bam1_core_t *c, const uint32_t *cigar)
{
uint32_t k, end;
int32_t i = 1, name_len;
// check EOF
i = bgzf_check_EOF(fp);
- if (i < 0) fprintf(stderr, "[bam_header_read] read from pipe; skip EOF checking.\n");
+ if (i < 0) {
+ // If the file is a pipe, checking the EOF marker will *always* fail
+ // with ESPIPE. Suppress the error message in this case.
+ if (errno != ESPIPE) perror("[bam_header_read] bgzf_check_EOF");
+ }
else if (i == 0) fprintf(stderr, "[bam_header_read] EOF marker is absent.\n");
// read "BAM1"
if (bam_read(fp, buf, 4) != 4) return 0;