New upstream release.

[samtools.git] / sam.c

diff --git a/sam.c b/sam.c
index ad4325bb4b8e8436d21e921478ed00467aac0e6b..f026bc80864dbc75557bf632c760978e54acc453 100644 (file)
--- a/sam.c
+++ b/sam.c
@@ -40,9 +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;
@@ -55,18 +55,23 @@ 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);
                                }
-                               if (fp->header->n_targets == 0)
+                               if (fp->header->n_targets == 0 && bam_verbose >= 1)
                                        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);
+                       } else if (bam_verbose >= 2) fprintf(stderr, "[samopen] SAM header is present: %d sequences.\n", fp->header->n_targets);
                }
-       } 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;
@@ -75,11 +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 
@@ -88,10 +93,10 @@ samfile_t *samopen(const char *fn, const char *mode, const void *aux)
                                sam_header_parse(alt);
                                alt->l_text = 0; alt->text = 0;
                                // check if there are @SQ lines in the header
-                               fwrite(fp->header->text, 1, fp->header->l_text, fp->x.tamw);
+                               fwrite(fp->header->text, 1, fp->header->l_text, fp->x.tamw); // FIXME: better to skip the trailing NULL
                                if (alt->n_targets) { // then write the header text without dumping ->target_{name,len}
-                                       if (alt->n_targets != fp->header->n_targets)
-                                               fprintf(stderr, "[samopen] inconsistent number of target sequences.\n");
+                                       if (alt->n_targets != fp->header->n_targets && bam_verbose >= 1)
+                                               fprintf(stderr, "[samopen] inconsistent number of target sequences. Output the text header.\n");
                                } else { // then dump ->target_{name,len}
                                        for (i = 0; i < fp->header->n_targets; ++i)
                                                fprintf(fp->x.tamw, "@SQ\tSN:%s\tLN:%d\n", fp->header->target_name[i], fp->header->target_len[i]);
@@ -163,7 +168,7 @@ char *samfaipath(const char *fn_ref)
                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 (bam_verbose >= 3) 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;