# Uploaded samtools version 0.1.14-1.

[samtools.git] / sam.c

diff --git a/sam.c b/sam.c
index a74c557bad9aa83d274ea44bdfe1a16dfbc4d5a6..e195b0f13e93d018d05f0784fc76c437e2eec8cd 100644 (file)
--- a/sam.c
+++ b/sam.c
@@ -12,7 +12,7 @@ bam_header_t *bam_header_dup(const bam_header_t *h0)
        int i;
        h = bam_header_init();
        *h = *h0;
-       h->hash = 0;
+       h->hash = h->dict = h->rg2lib = 0;
        h->text = (char*)calloc(h->l_text + 1, 1);
        memcpy(h->text, h0->text, h->l_text);
        h->target_len = (uint32_t*)calloc(h->n_targets, 4);
@@ -21,7 +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)
@@ -41,9 +40,9 @@ samfile_t *samopen(const char *fn, const char *mode, const void *aux)
 {
        samfile_t *fp;
        fp = (samfile_t*)calloc(1, sizeof(samfile_t));
-       if (mode[0] == 'r') { // read
+       if (strchr(mode, 'r')) { // read
                fp->type |= TYPE_READ;
-               if (mode[1] == 'b') { // binary
+               if (strchr(mode, 'b')) { // binary
                        fp->type |= TYPE_BAM;
                        fp->x.bam = strcmp(fn, "-")? bam_open(fn, "r") : bam_dopen(fileno(stdin), "r");
                        if (fp->x.bam == 0) goto open_err_ret;
@@ -56,6 +55,7 @@ samfile_t *samopen(const char *fn, const char *mode, const void *aux)
                                if (aux) { // check if aux is present
                                        bam_header_t *textheader = fp->header;
                                        fp->header = sam_header_read2((const char*)aux);
+                                       if (fp->header == 0) goto open_err_ret;
                                        append_header_text(fp->header, textheader->text, textheader->l_text);
                                        bam_header_destroy(textheader);
                                }
@@ -63,12 +63,15 @@ samfile_t *samopen(const char *fn, const char *mode, const void *aux)
                                        fprintf(stderr, "[samopen] no @SQ lines in the header.\n");
                        } else fprintf(stderr, "[samopen] SAM header is present: %d sequences.\n", fp->header->n_targets);
                }
-               sam_header_parse_rg(fp->header);
-       } else if (mode[0] == 'w') { // write
+       } else if (strchr(mode, 'w')) { // write
                fp->header = bam_header_dup((const bam_header_t*)aux);
-               if (mode[1] == 'b') { // binary
+               if (strchr(mode, 'b')) { // binary
                        char bmode[3];
-                       bmode[0] = 'w'; bmode[1] = strstr(mode, "u")? 'u' : 0; bmode[2] = 0;
+                       int i, compress_level = -1;
+                       for (i = 0; mode[i]; ++i) if (mode[i] >= '0' && mode[i] <= '9') break;
+                       if (mode[i]) compress_level = mode[i] - '0';
+                       if (strchr(mode, 'u')) compress_level = 0;
+                       bmode[0] = 'w'; bmode[1] = compress_level < 0? 0 : compress_level + '0'; bmode[2] = 0;
                        fp->type |= TYPE_BAM;
                        fp->x.bam = strcmp(fn, "-")? bam_open(fn, bmode) : bam_dopen(fileno(stdout), bmode);
                        if (fp->x.bam == 0) goto open_err_ret;
@@ -77,11 +80,11 @@ 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 |= BAM_OFSTR<<2;
-                       else if (strstr(mode, "x")) fp->type |= BAM_OFHEX<<2;
+                       if (strchr(mode, 'X')) fp->type |= BAM_OFSTR<<2;
+                       else if (strchr(mode, 'x')) fp->type |= BAM_OFHEX<<2;
                        else fp->type |= BAM_OFDEC<<2;
                        // write header
-                       if (strstr(mode, "h")) {
+                       if (strchr(mode, 'h')) {
                                int i;
                                bam_header_t *alt;
                                // parse the header text