* This revision is SERIOUSLY BUGGY. Please NOT use it.

[samtools.git] / sam.c

diff --git a/sam.c b/sam.c
index a3f2998687beb573186457837a844150e6245209..07524c0213b30bcae3870f8424da38daef43ac49 100644 (file)
--- a/sam.c
+++ b/sam.c
@@ -1,9 +1,10 @@
 #include <string.h>
+#include <unistd.h>
+#include "faidx.h"
 #include "sam.h"
 
 #define TYPE_BAM  1
 #define TYPE_READ 2
-#define TYPE_HEX  4
 
 bam_header_t *bam_header_dup(const bam_header_t *h0)
 {
@@ -20,7 +21,6 @@ bam_header_t *bam_header_dup(const bam_header_t *h0)
                h->target_len[i] = h0->target_len[i];
                h->target_name[i] = strdup(h0->target_name[i]);
        }
-       if (h0->rg2lib) h->rg2lib = bam_strmap_dup(h0->rg2lib);
        return h;
 }
 static void append_header_text(bam_header_t *header, char* text, int len)
@@ -76,7 +76,9 @@ samfile_t *samopen(const char *fn, const char *mode, const void *aux)
                        // open file
                        fp->x.tamw = strcmp(fn, "-")? fopen(fn, "w") : stdout;
                        if (fp->x.tamr == 0) goto open_err_ret;
-                       if (strstr(mode, "x")) fp->type |= TYPE_HEX;
+                       if (strstr(mode, "X")) fp->type |= BAM_OFSTR<<2;
+                       else if (strstr(mode, "x")) fp->type |= BAM_OFHEX<<2;
+                       else fp->type |= BAM_OFDEC<<2;
                        // write header
                        if (strstr(mode, "h")) {
                                int i;
@@ -128,7 +130,7 @@ int samwrite(samfile_t *fp, const bam1_t *b)
        if (fp == 0 || (fp->type & TYPE_READ)) return -1; // not open for writing
        if (fp->type & TYPE_BAM) return bam_write1(fp->x.bam, b);
        else {
-               char *s = bam_format1_core(fp->header, b, fp->type & TYPE_HEX);
+               char *s = bam_format1_core(fp->header, b, fp->type>>2&3);
                int l = strlen(s);
                fputs(s, fp->x.tamw); fputc('\n', fp->x.tamw);
                free(s);
@@ -151,3 +153,23 @@ int sampileup(samfile_t *fp, int mask, bam_pileup_f func, void *func_data)
        bam_destroy1(b);
        return 0;
 }
+
+char *samfaipath(const char *fn_ref)
+{
+       char *fn_list = 0;
+       if (fn_ref == 0) return 0;
+       fn_list = calloc(strlen(fn_ref) + 5, 1);
+       strcat(strcpy(fn_list, fn_ref), ".fai");
+       if (access(fn_list, R_OK) == -1) { // fn_list is unreadable
+               if (access(fn_ref, R_OK) == -1) {
+                       fprintf(stderr, "[samfaipath] fail to read file %s.\n", fn_ref);
+               } else {
+                       fprintf(stderr, "[samfaipath] build FASTA index...\n");
+                       if (fai_build(fn_ref) == -1) {
+                               fprintf(stderr, "[samfaipath] fail to build FASTA index.\n");
+                               free(fn_list); fn_list = 0;
+                       }
+               }
+       }
+       return fn_list;
+}