Imported Upstream version 0.1.6~dfsg

[samtools.git] / bam.c

diff --git a/bam.c b/bam.c
index 1ff4a5aba25028f4fccdd0735a9dcae594b6e9a8..619b46a6718a773aa073e7ecede13ef5cd10dee8 100644 (file)
--- a/bam.c
+++ b/bam.c
@@ -6,6 +6,7 @@
 #include "kstring.h"
 
 int bam_is_be = 0;
+char *bam_flag2char_table = "pPuUrR12sfd\0\0\0\0\0";
 
 /**************************
  * CIGAR related routines *
@@ -90,7 +91,11 @@ bam_header_t *bam_header_read(bamFile fp)
 {
        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) fprintf(stderr, "[bam_header_read] read from pipe; skip EOF checking.\n");
+       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)) {
@@ -236,7 +241,7 @@ int bam_write1(bamFile fp, const bam1_t *b)
        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;
@@ -244,7 +249,15 @@ char *bam_format1(const bam_header_t *header, const bam1_t *b)
        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);
@@ -258,10 +271,12 @@ char *bam_format1(const bam_header_t *header, const bam1_t *b)
        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];
@@ -282,6 +297,11 @@ char *bam_format1(const bam_header_t *header, const bam1_t *b)
        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);