From 431e646d3b2019312626cf111460ea3df7029962 Mon Sep 17 00:00:00 2001 From: Heng Li Date: Fri, 12 Jun 2009 20:25:50 +0000 Subject: [PATCH] * samtools-0.1.4-7 (r337) * bgzf.c: support mode string "wu": uncompressed output * "samtools view" support "-u" command-line option --- bamtk.c | 2 +- bgzf.c | 24 +++++++++++++----------- bgzf.h | 5 ++--- sam.c | 4 +++- sam_view.c | 13 +++++++++---- 5 files changed, 28 insertions(+), 20 deletions(-) diff --git a/bamtk.c b/bamtk.c index f762a13..878562c 100644 --- a/bamtk.c +++ b/bamtk.c @@ -3,7 +3,7 @@ #include "bam.h" #ifndef PACKAGE_VERSION -#define PACKAGE_VERSION "0.1.4-6 (r334)" +#define PACKAGE_VERSION "0.1.4-7 (r337)" #endif int bam_taf2baf(int argc, char *argv[]); diff --git a/bgzf.c b/bgzf.c index bffe8b5..49a78f1 100644 --- a/bgzf.c +++ b/bgzf.c @@ -9,6 +9,8 @@ * or functionality. */ +/* 2009-06-12 by lh3: support a mode string like "wu" where 'u' for uncompressed output */ + #include #include #include @@ -91,7 +93,7 @@ open_read(int fd) fp = malloc(sizeof(BGZF)); fp->file_descriptor = fd; fp->open_mode = 'r'; - fp->owned_file = 0; + fp->owned_file = 0; fp->is_uncompressed = 0; fp->file = file; fp->uncompressed_block_size = MAX_BLOCK_SIZE; fp->uncompressed_block = malloc(MAX_BLOCK_SIZE); @@ -106,7 +108,7 @@ open_read(int fd) static BGZF* -open_write(int fd) +open_write(int fd, bool is_uncompressed) { FILE* file = fdopen(fd, "w"); BGZF* fp; @@ -114,7 +116,7 @@ open_write(int fd) fp = malloc(sizeof(BGZF)); fp->file_descriptor = fd; fp->open_mode = 'w'; - fp->owned_file = 0; + fp->owned_file = 0; fp->is_uncompressed = is_uncompressed; fp->file = file; fp->uncompressed_block_size = DEFAULT_BLOCK_SIZE; fp->uncompressed_block = NULL; @@ -131,16 +133,16 @@ BGZF* bgzf_open(const char* __restrict path, const char* __restrict mode) { BGZF* fp = NULL; - if (strcasecmp(mode, "r") == 0) { + if (mode[0] == 'r' || mode[0] == 'R') { /* The reading mode is preferred. */ int oflag = O_RDONLY; int fd = open(path, oflag); if (fd == -1) return 0; fp = open_read(fd); - } else if (strcasecmp(mode, "w") == 0) { + } else if (mode[0] == 'w' || mode[0] == 'W') { int oflag = O_WRONLY | O_CREAT | O_TRUNC; int fd = open(path, oflag, 0644); if (fd == -1) return 0; - fp = open_write(fd); + fp = open_write(fd, strstr(mode, "u")? 1 : 0); } if (fp != NULL) { fp->owned_file = 1; @@ -152,10 +154,10 @@ BGZF* bgzf_fdopen(int fd, const char * __restrict mode) { if (fd == -1) return 0; - if (strcasecmp(mode, "r") == 0) { + if (mode[0] == 'r' || mode[0] == 'R') { return open_read(fd); - } else if (strcasecmp(mode, "w") == 0) { - return open_write(fd); + } else if (mode[0] == 'w' || mode[0] == 'W') { + return open_write(fd, strstr(mode, "u")? 1 : 0); } else { return NULL; } @@ -195,7 +197,7 @@ deflate_block(BGZF* fp, int block_length) int input_length = block_length; int compressed_length = 0; while (1) { - + int compress_level = fp->is_uncompressed? 0 : Z_DEFAULT_COMPRESSION; z_stream zs; zs.zalloc = NULL; zs.zfree = NULL; @@ -204,7 +206,7 @@ deflate_block(BGZF* fp, int block_length) zs.next_out = (void*)&buffer[BLOCK_HEADER_LENGTH]; zs.avail_out = buffer_size - BLOCK_HEADER_LENGTH - BLOCK_FOOTER_LENGTH; - int status = deflateInit2(&zs, Z_DEFAULT_COMPRESSION, Z_DEFLATED, + int status = deflateInit2(&zs, compress_level, Z_DEFLATED, GZIP_WINDOW_BITS, Z_DEFAULT_MEM_LEVEL, Z_DEFAULT_STRATEGY); if (status != Z_OK) { report_error(fp, "deflate init failed"); diff --git a/bgzf.h b/bgzf.h index 7e76bcb..ca5e7ab 100644 --- a/bgzf.h +++ b/bgzf.h @@ -14,16 +14,15 @@ #include #include -#include "zlib.h" #include -//#include "zutil.h" +#include //typedef int8_t bool; typedef struct { int file_descriptor; char open_mode; // 'r' or 'w' - bool owned_file; + bool owned_file, is_uncompressed; FILE* file; int uncompressed_block_size; int compressed_block_size; diff --git a/sam.c b/sam.c index 9a6e201..04be5c5 100644 --- a/sam.c +++ b/sam.c @@ -49,8 +49,10 @@ samfile_t *samopen(const char *fn, const char *mode, const void *aux) } else if (mode[0] == 'w') { // write fp->header = bam_header_dup((const bam_header_t*)aux); if (mode[1] == 'b') { // binary + char bmode[3]; + bmode[0] = 'w'; bmode[1] = strstr(mode, "u")? 'u' : 0; bmode[2] = 0; fp->type |= TYPE_BAM; - fp->x.bam = strcmp(fn, "-")? bam_open(fn, "w") : bam_dopen(fileno(stdout), "w"); + fp->x.bam = strcmp(fn, "-")? bam_open(fn, bmode) : bam_dopen(fileno(stdout), bmode); if (fp->x.bam == 0) goto open_err_ret; bam_header_write(fp->x.bam, fp->header); } else { // text diff --git a/sam_view.c b/sam_view.c index 5bd679c..4858610 100644 --- a/sam_view.c +++ b/sam_view.c @@ -20,16 +20,16 @@ static int usage(void); int main_samview(int argc, char *argv[]) { - int c, is_header = 0, is_header_only = 0, is_bamin = 1, ret = 0; + int c, is_header = 0, is_header_only = 0, is_bamin = 1, ret = 0, is_uncompressed = 0, is_bamout = 0; samfile_t *in = 0, *out = 0; - char in_mode[4], out_mode[4], *fn_out = 0, *fn_list = 0; + char in_mode[5], out_mode[5], *fn_out = 0, *fn_list = 0; /* parse command-line options */ strcpy(in_mode, "r"); strcpy(out_mode, "w"); - while ((c = getopt(argc, argv, "Sbt:hHo:q:f:F:")) >= 0) { + while ((c = getopt(argc, argv, "Sbt:hHo:q:f:F:u")) >= 0) { switch (c) { case 'S': is_bamin = 0; break; - case 'b': strcat(out_mode, "b"); break; + case 'b': is_bamout = 1; break; case 't': fn_list = strdup(optarg); is_bamin = 0; break; case 'h': is_header = 1; break; case 'H': is_header_only = 1; break; @@ -37,12 +37,16 @@ int main_samview(int argc, char *argv[]) case 'f': g_flag_on = strtol(optarg, 0, 0); break; case 'F': g_flag_off = strtol(optarg, 0, 0); break; case 'q': g_min_mapQ = atoi(optarg); break; + case 'u': is_uncompressed = 1; break; default: return usage(); } } + if (is_uncompressed) is_bamout = 1; if (is_header_only) is_header = 1; + if (is_bamout) strcat(out_mode, "b"); if (is_bamin) strcat(in_mode, "b"); if (is_header) strcat(out_mode, "h"); + if (is_uncompressed) strcat(out_mode, "u"); if (argc == optind) return usage(); // open file handlers @@ -101,6 +105,7 @@ static int usage() fprintf(stderr, " -h print header for the SAM output\n"); fprintf(stderr, " -H print header only (no alignments)\n"); fprintf(stderr, " -S input is SAM\n"); + fprintf(stderr, " -u uncompressed BAM output (force -b)\n"); fprintf(stderr, " -t FILE list of reference names and lengths (force -S) [null]\n"); fprintf(stderr, " -o FILE output file name [stdout]\n"); fprintf(stderr, " -f INT required flag, 0 for unset [0]\n"); -- 2.39.2