Merge commit 'upstream/0.1.15'

[samtools.git] / bam_sort.c

diff --git a/bam_sort.c b/bam_sort.c
index 38f15d655c253dc1f7e8cd50dd39c178c448f584..94970b5f9e1c0f9ef76a73fcdda12e8a633a3ff2 100644 (file)
--- a/bam_sort.c
+++ b/bam_sort.c
@@ -70,6 +70,7 @@ static void swap_header_text(bam_header_t *h1, bam_header_t *h2)
 
 #define MERGE_RG     1
 #define MERGE_UNCOMP 2
+#define MERGE_LEVEL1 4
 
 /*!
   @abstract    Merge multiple sorted BAM.
@@ -207,11 +208,9 @@ int bam_merge_core(int by_qname, const char *out, const char *headers, int n, ch
                }
                else h->pos = HEAP_EMPTY;
        }
-       if (flag & MERGE_UNCOMP) {
-               fpout = strcmp(out, "-")? bam_open(out, "wu") : bam_dopen(fileno(stdout), "wu");
-       } else {
-               fpout = strcmp(out, "-")? bam_open(out, "w") : bam_dopen(fileno(stdout), "w");
-       }
+       if (flag & MERGE_UNCOMP) fpout = strcmp(out, "-")? bam_open(out, "wu") : bam_dopen(fileno(stdout), "wu");
+       else if (flag & MERGE_LEVEL1) fpout = strcmp(out, "-")? bam_open(out, "w1") : bam_dopen(fileno(stdout), "w1");
+       else fpout = strcmp(out, "-")? bam_open(out, "w") : bam_dopen(fileno(stdout), "w");
        if (fpout == 0) {
                fprintf(stderr, "[%s] fail to create the output file.\n", __func__);
                return -1;
@@ -257,11 +256,12 @@ int bam_merge(int argc, char *argv[])
        int c, is_by_qname = 0, flag = 0, ret = 0;
        char *fn_headers = NULL, *reg = 0;
 
-       while ((c = getopt(argc, argv, "h:nruR:")) >= 0) {
+       while ((c = getopt(argc, argv, "h:nru1R:")) >= 0) {
                switch (c) {
                case 'r': flag |= MERGE_RG; break;
                case 'h': fn_headers = strdup(optarg); break;
                case 'n': is_by_qname = 1; break;
+               case '1': flag |= MERGE_LEVEL1; break;
                case 'u': flag |= MERGE_UNCOMP; break;
                case 'R': reg = strdup(optarg); break;
                }
@@ -272,6 +272,7 @@ int bam_merge(int argc, char *argv[])
                fprintf(stderr, "Options: -n       sort by read names\n");
                fprintf(stderr, "         -r       attach RG tag (inferred from file names)\n");
                fprintf(stderr, "         -u       uncompressed BAM output\n");
+               fprintf(stderr, "         -1       compress level 1\n");
                fprintf(stderr, "         -R STR   merge file in the specified region STR [all]\n");
                fprintf(stderr, "         -h FILE  copy the header in FILE to <out.bam> [in1.bam]\n\n");
                fprintf(stderr, "Note: Samtools' merge does not reconstruct the @RG dictionary in the header. Users\n");
@@ -298,14 +299,19 @@ KSORT_INIT(sort, bam1_p, bam1_lt)
 
 static void sort_blocks(int n, int k, bam1_p *buf, const char *prefix, const bam_header_t *h, int is_stdout)
 {
-       char *name;
+       char *name, mode[3];
        int i;
        bamFile fp;
        ks_mergesort(sort, k, buf, 0);
        name = (char*)calloc(strlen(prefix) + 20, 1);
-       if (n >= 0) sprintf(name, "%s.%.4d.bam", prefix, n);
-       else sprintf(name, "%s.bam", prefix);
-       fp = is_stdout? bam_dopen(fileno(stdout), "w") : bam_open(name, "w");
+       if (n >= 0) {
+               sprintf(name, "%s.%.4d.bam", prefix, n);
+               strcpy(mode, "w1");
+       } else {
+               sprintf(name, "%s.bam", prefix);
+               strcpy(mode, "w");
+       }
+       fp = is_stdout? bam_dopen(fileno(stdout), mode) : bam_open(name, mode);
        if (fp == 0) {
                fprintf(stderr, "[sort_blocks] fail to create file %s.\n", name);
                free(name);