From: Heng Li Date: Thu, 22 Mar 2012 00:39:15 +0000 (-0400) Subject: control compression level at command line X-Git-Url: https://git.donarmstrong.com/?p=samtools.git;a=commitdiff_plain;h=d07731e7c769ac5f2709ac60eb60ddd3fa0120fd control compression level at command line --- diff --git a/bam_sort.c b/bam_sort.c index d38c7a1..6c3f52d 100644 --- 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] \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; }