#include <stdio.h>
#include <ctype.h>
+#include <errno.h>
+#include <assert.h>
#include "bam.h"
#include "bam_endian.h"
#include "kstring.h"
+#include "sam_header.h"
int bam_is_be = 0;
+char *bam_flag2char_table = "pPuUrR12sfd\0\0\0\0\0";
/**************************
* 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;
free(header->target_len);
}
free(header->text);
-#ifndef BAM_NO_HASH
- if (header->rg2lib) bam_strmap_destroy(header->rg2lib);
+ if (header->dict) sam_header_free(header->dict);
+ if (header->rg2lib) sam_tbl_destroy(header->rg2lib);
bam_destroy_header_hash(header);
-#endif
free(header);
}
{
bam_header_t *header;
char buf[4];
- int32_t i, name_len;
+ int32_t i = 1, name_len;
+ // check EOF
+ i = bgzf_check_EOF(fp);
+ 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;
if (strncmp(buf, "BAM\001", 4)) {
return bam_write1_core(fp, &b->core, b->data_len, b->data);
}
-char *bam_format1(const bam_header_t *header, const bam1_t *b)
+char *bam_format1_core(const bam_header_t *header, const bam1_t *b, int of)
{
uint8_t *s = bam1_seq(b), *t = bam1_qual(b);
int i;
kstring_t str;
str.l = str.m = 0; str.s = 0;
- ksprintf(&str, "%s\t%d\t", bam1_qname(b), c->flag);
+ ksprintf(&str, "%s\t", bam1_qname(b));
+ if (of == BAM_OFDEC) ksprintf(&str, "%d\t", c->flag);
+ else if (of == BAM_OFHEX) ksprintf(&str, "0x%x\t", c->flag);
+ else { // BAM_OFSTR
+ for (i = 0; i < 16; ++i)
+ if ((c->flag & 1<<i) && bam_flag2char_table[i])
+ kputc(bam_flag2char_table[i], &str);
+ kputc('\t', &str);
+ }
if (c->tid < 0) kputs("*\t", &str);
else ksprintf(&str, "%s\t", header->target_name[c->tid]);
ksprintf(&str, "%d\t%d\t", c->pos + 1, c->qual);
else if (c->mtid == c->tid) kputs("=\t", &str);
else ksprintf(&str, "%s\t", header->target_name[c->mtid]);
ksprintf(&str, "%d\t%d\t", c->mpos + 1, c->isize);
- for (i = 0; i < c->l_qseq; ++i) kputc(bam_nt16_rev_table[bam1_seqi(s, i)], &str);
- kputc('\t', &str);
- if (t[0] == 0xff) kputc('*', &str);
- else for (i = 0; i < c->l_qseq; ++i) kputc(t[i] + 33, &str);
+ if (c->l_qseq) {
+ for (i = 0; i < c->l_qseq; ++i) kputc(bam_nt16_rev_table[bam1_seqi(s, i)], &str);
+ kputc('\t', &str);
+ if (t[0] == 0xff) kputc('*', &str);
+ else for (i = 0; i < c->l_qseq; ++i) kputc(t[i] + 33, &str);
+ } else ksprintf(&str, "*\t*");
s = bam1_aux(b);
while (s < b->data + b->data_len) {
uint8_t type, key[2];
return str.s;
}
+char *bam_format1(const bam_header_t *header, const bam1_t *b)
+{
+ return bam_format1_core(header, b, BAM_OFDEC);
+}
+
void bam_view1(const bam_header_t *header, const bam1_t *b)
{
char *s = bam_format1(header, b);
printf("%s\n", s);
+ free(s);
+}
+
+// FIXME: we should also check the LB tag associated with each alignment
+const char *bam_get_library(bam_header_t *h, const bam1_t *b)
+{
+ const uint8_t *rg;
+ if (h->dict == 0) h->dict = sam_header_parse2(h->text);
+ if (h->rg2lib == 0) h->rg2lib = sam_header2tbl(h->dict, "RG", "ID", "LB");
+ rg = bam_aux_get(b, "RG");
+ return (rg == 0)? 0 : sam_tbl_get(h->rg2lib, (const char*)(rg + 1));
}