Starting the work on next package update.

[samtools.git] / bam.c

diff --git a/bam.c b/bam.c
index 96aace21c7ab7c261380ee2136e283022e9c834d..0055e8427667dd95151ea1a1bef5dd14e74e15f1 100644 (file)
--- a/bam.c
+++ b/bam.c
@@ -7,7 +7,7 @@
 #include "kstring.h"
 #include "sam_header.h"
 
-int bam_is_be = 0;
+int bam_is_be = 0, bam_verbose = 2;
 char *bam_flag2char_table = "pPuUrR12sfd\0\0\0\0\0";
 
 /**************************
@@ -32,7 +32,7 @@ int32_t bam_cigar2qlen(const bam1_core_t *c, const uint32_t *cigar)
        int32_t l = 0;
        for (k = 0; k < c->n_cigar; ++k) {
                int op = cigar[k] & BAM_CIGAR_MASK;
-               if (op == BAM_CMATCH || op == BAM_CINS || op == BAM_CSOFT_CLIP)
+               if (op == BAM_CMATCH || op == BAM_CINS || op == BAM_CSOFT_CLIP || op == BAM_CEQUAL || op == BAM_CDIFF)
                        l += cigar[k] >> BAM_CIGAR_SHIFT;
        }
        return l;
@@ -160,6 +160,19 @@ static void swap_endian_data(const bam1_core_t *c, int data_len, uint8_t *data)
                else if (type == 'I' || type == 'F') { bam_swap_endian_4p(s); s += 4; }
                else if (type == 'D') { bam_swap_endian_8p(s); s += 8; }
                else if (type == 'Z' || type == 'H') { while (*s) ++s; ++s; }
+               else if (type == 'B') {
+                       int32_t n, Bsize = bam_aux_type2size(*s);
+                       memcpy(&n, s + 1, 4);
+                       if (1 == Bsize) {
+                       } else if (2 == Bsize) {
+                               for (i = 0; i < n; i += 2)
+                                       bam_swap_endian_2p(s + 5 + i);
+                       } else if (4 == Bsize) {
+                               for (i = 0; i < n; i += 4)
+                                       bam_swap_endian_4p(s + 5 + i);
+                       }
+                       bam_swap_endian_4p(s+1); 
+               }
        }
 }
 
@@ -255,7 +268,7 @@ char *bam_format1_core(const bam_header_t *header, const bam1_t *b, int of)
        else {
                for (i = 0; i < c->n_cigar; ++i) {
                        kputw(bam1_cigar(b)[i]>>BAM_CIGAR_SHIFT, &str);
-                       kputc("MIDNSHP"[bam1_cigar(b)[i]&BAM_CIGAR_MASK], &str);
+                       kputc("MIDNSHP=X"[bam1_cigar(b)[i]&BAM_CIGAR_MASK], &str);
                }
        }
        kputc('\t', &str);
@@ -289,6 +302,23 @@ char *bam_format1_core(const bam_header_t *header, const bam1_t *b, int of)
                else if (type == 'f') { ksprintf(&str, "f:%g", *(float*)s); s += 4; }
                else if (type == 'd') { ksprintf(&str, "d:%lg", *(double*)s); s += 8; }
                else if (type == 'Z' || type == 'H') { kputc(type, &str); kputc(':', &str); while (*s) kputc(*s++, &str); ++s; }
+               else if (type == 'B') {
+                       uint8_t sub_type = *(s++);
+                       int32_t n;
+                       memcpy(&n, s, 4);
+                       s += 4; // no point to the start of the array
+                       kputc(type, &str); kputc(':', &str); kputc(sub_type, &str); // write the typing
+                       for (i = 0; i < n; ++i) {
+                               kputc(',', &str);
+                               if ('c' == sub_type || 'c' == sub_type) { kputw(*(int8_t*)s, &str); ++s; }
+                               else if ('C' == sub_type) { kputw(*(uint8_t*)s, &str); ++s; }
+                               else if ('s' == sub_type) { kputw(*(int16_t*)s, &str); s += 2; }
+                               else if ('S' == sub_type) { kputw(*(uint16_t*)s, &str); s += 2; }
+                               else if ('i' == sub_type) { kputw(*(int32_t*)s, &str); s += 4; }
+                               else if ('I' == sub_type) { kputuw(*(uint32_t*)s, &str); s += 4; }
+                               else if ('f' == sub_type) { ksprintf(&str, "%g", *(float*)s); s += 4; }
+                       }
+               }
        }
        return str.s;
 }