control compression level at command line

diff --git a/bam_sort.c b/bam_sort.c
index d38c7a11f8d22a74d30e5862b1d5440ba1a0e474..6c3f52d17ce4dc0dfd8c9d1277cf8050c7e267ca 100644 (file)
--- a/bam_sort.c
+++ b/bam_sort.c
@@ -89,7 +89,7 @@ static void swap_header_text(bam_header_t *h1, bam_header_t *h2)
   @discussion Padding information may NOT correctly maintained. This
   function is NOT thread safe.
  */
-int bam_merge_core2(int by_qname, const char *out, const char *headers, int n, char * const *fn, int flag, const char *reg, int n_threads)
+int bam_merge_core2(int by_qname, const char *out, const char *headers, int n, char * const *fn, int flag, const char *reg, int n_threads, int level)
 {
        bamFile fpout, *fp;
        heap1_t *heap;
@@ -97,7 +97,7 @@ int bam_merge_core2(int by_qname, const char *out, const char *headers, int n, c
        bam_header_t *hheaders = NULL;
        int i, j, *RG_len = 0;
        uint64_t idx = 0;
-       char **RG = 0;
+       char **RG = 0, mode[8];
        bam_iter_t *iter = 0;
 
        if (headers) {
@@ -212,10 +212,11 @@ int bam_merge_core2(int by_qname, const char *out, const char *headers, int n, c
                }
                else h->pos = HEAP_EMPTY;
        }
-       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) {
+       if (flag & MERGE_UNCOMP) level = 0;
+       else if (flag & MERGE_LEVEL1) level = 1;
+       strcpy(mode, "w");
+       if (level >= 0) sprintf(mode + 1, "%d", level < 9? level : 9);
+       if ((fpout = strcmp(out, "-")? bam_open(out, "w") : bam_dopen(fileno(stdout), "w")) == 0) {
                fprintf(stderr, "[%s] fail to create the output file.\n", __func__);
                return -1;
        }
@@ -258,15 +259,15 @@ int bam_merge_core2(int by_qname, const char *out, const char *headers, int n, c
 
 int bam_merge_core(int by_qname, const char *out, const char *headers, int n, char * const *fn, int flag, const char *reg)
 {
-       return bam_merge_core2(by_qname, out, headers, n, fn, flag, reg, 0);
+       return bam_merge_core2(by_qname, out, headers, n, fn, flag, reg, 0, -1);
 }
 
 int bam_merge(int argc, char *argv[])
 {
-       int c, is_by_qname = 0, flag = 0, ret = 0, n_threads = 0;
+       int c, is_by_qname = 0, flag = 0, ret = 0, n_threads = 0, level = -1;
        char *fn_headers = NULL, *reg = 0;
 
-       while ((c = getopt(argc, argv, "h:nru1R:f@:")) >= 0) {
+       while ((c = getopt(argc, argv, "h:nru1R:f@:l:")) >= 0) {
                switch (c) {
                case 'r': flag |= MERGE_RG; break;
                case 'f': flag |= MERGE_FORCE; break;
@@ -275,6 +276,7 @@ int bam_merge(int argc, char *argv[])
                case '1': flag |= MERGE_LEVEL1; break;
                case 'u': flag |= MERGE_UNCOMP; break;
                case 'R': reg = strdup(optarg); break;
+               case 'l': level = atoi(optarg); break;
                case '@': n_threads = atoi(optarg); break;
                }
        }
@@ -302,7 +304,7 @@ int bam_merge(int argc, char *argv[])
                        return 1;
                }
        }
-       if (bam_merge_core2(is_by_qname, argv[optind], fn_headers, argc - optind - 1, argv + optind + 1, flag, reg, n_threads) < 0) ret = 1;
+       if (bam_merge_core2(is_by_qname, argv[optind], fn_headers, argc - optind - 1, argv + optind + 1, flag, reg, n_threads, level) < 0) ret = 1;
        free(reg);
        free(fn_headers);
        return ret;
@@ -402,7 +404,7 @@ static int sort_blocks(int n_files, size_t k, bam1_p *buf, const char *prefix, c
   and then merge them by calling bam_merge_core(). This function is
   NOT thread safe.
  */
-void bam_sort_core_ext(int is_by_qname, const char *fn, const char *prefix, size_t _max_mem, int is_stdout, int n_threads)
+void bam_sort_core_ext(int is_by_qname, const char *fn, const char *prefix, size_t _max_mem, int is_stdout, int n_threads, int level)
 {
        int ret, i, extra_mem, n_files = 0;
        size_t mem, max_k, k, max_mem;
@@ -449,8 +451,11 @@ void bam_sort_core_ext(int is_by_qname, const char *fn, const char *prefix, size
        else sprintf(fnout, "%s.bam", prefix);
        // write the final output
        if (n_files == 0) { // a single block
+               char mode[8];
+               strcpy(mode, "w");
+               if (level >= 0) sprintf(mode + 1, "%d", level < 9? level : 9);
                ks_mergesort(sort, k, buf, 0);
-               write_buffer(fnout, "w", k, buf, header, n_threads);
+               write_buffer(fnout, mode, k, buf, header, n_threads);
        } else { // then merge
                char **fns;
                n_files = sort_blocks(n_files, k, buf, prefix, header, n_threads);
@@ -460,7 +465,7 @@ void bam_sort_core_ext(int is_by_qname, const char *fn, const char *prefix, size
                        fns[i] = (char*)calloc(strlen(prefix) + 20, 1);
                        sprintf(fns[i], "%s.%.4d.bam", prefix, i);
                }
-               bam_merge_core2(is_by_qname, fnout, 0, n_files, fns, 0, 0, n_threads);
+               bam_merge_core2(is_by_qname, fnout, 0, n_files, fns, 0, 0, n_threads, level);
                for (i = 0; i < n_files; ++i) {
                        unlink(fns[i]);
                        free(fns[i]);
@@ -481,14 +486,14 @@ void bam_sort_core_ext(int is_by_qname, const char *fn, const char *prefix, size
 
 void bam_sort_core(int is_by_qname, const char *fn, const char *prefix, size_t max_mem)
 {
-       bam_sort_core_ext(is_by_qname, fn, prefix, max_mem, 0, 0);
+       bam_sort_core_ext(is_by_qname, fn, prefix, max_mem, 0, 0, -1);
 }
 
 int bam_sort(int argc, char *argv[])
 {
        size_t max_mem = 768<<20; // 512MB
-       int c, is_by_qname = 0, is_stdout = 0, n_threads = 0;
-       while ((c = getopt(argc, argv, "nom:@:")) >= 0) {
+       int c, is_by_qname = 0, is_stdout = 0, n_threads = 0, level = -1;
+       while ((c = getopt(argc, argv, "nom:@:l:")) >= 0) {
                switch (c) {
                case 'o': is_stdout = 1; break;
                case 'n': is_by_qname = 1; break;
@@ -501,12 +506,13 @@ int bam_sort(int argc, char *argv[])
                                break;
                        }
                case '@': n_threads = atoi(optarg); break;
+               case 'l': level = atoi(optarg); break;
                }
        }
        if (optind + 2 > argc) {
                fprintf(stderr, "Usage: samtools sort [-on] [-m maxMem=1G] <in.bam> <out.prefix>\n");
                return 1;
        }
-       bam_sort_core_ext(is_by_qname, argv[optind], argv[optind+1], max_mem, is_stdout, n_threads);
+       bam_sort_core_ext(is_by_qname, argv[optind], argv[optind+1], max_mem, is_stdout, n_threads, level);
        return 0;
 }