diff srf2fastq/io_lib-1.12.2/progs/srf_list.c @ 0:d901c9f41a6a default tip

Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/srf2fastq/io_lib-1.12.2/progs/srf_list.c	Tue Jun 07 17:48:05 2011 -0400
@@ -0,0 +1,166 @@
+#ifdef HAVE_CONFIG_H
+#include "io_lib_config.h"
+#endif
+
+#include <stdio.h>
+#include <string.h>
+#include <stdlib.h>
+#include <errno.h>
+#include <unistd.h>
+#include <inttypes.h>
+
+#include <io_lib/os.h>
+#include <io_lib/hash_table.h>
+#include <io_lib/srf.h>
+
+/* Command line options */
+typedef struct {
+    int long_format;
+    int count_only;
+    int verbose;
+} opts;
+
+/*
+ * Lists the contents of an SRF file.
+ *
+ * Returns num_reads for success
+ *        -1 for failure
+ */
+int64_t list_file(char *fname, opts *opts) {
+    srf_t *srf;
+    char name[512];
+    int64_t count = 0;
+    int type;
+    uint64_t pos;
+
+    if (NULL == (srf = srf_open(fname, "r"))) {
+	perror(fname);
+	return -1;
+    }
+
+    /* Scan through file gathering the details to index in memory */
+    while ((type = srf_next_block_details(srf, &pos, name)) >= 0) {
+	if (type == SRFB_TRACE_BODY) {
+	    count++;
+	    if (!opts->count_only) {
+		if (opts->long_format)
+		    printf("%-30s %10"PRId64" + %4d + %5d\n",
+			   name, pos,
+			   srf->tb.trace_size,
+			   srf->th.trace_hdr_size);
+		else
+		    puts(name);
+	    }
+	}
+    }
+
+    srf_destroy(srf, 1);
+
+    return count;
+}
+
+/*
+ * Counts the contents of an SRF file.
+ * If the hash index exists it uses this instead.
+ *
+ * Returns num_reads for success
+ *        -1 for failure
+ */
+int64_t count_file(char *fname, opts *opts) {
+    srf_t *srf;
+    srf_index_hdr_t hdr;
+    int64_t count = 0;
+    off_t ipos, skip;
+    int item_sz = 9, i;
+    unsigned char data[16];
+
+    if (NULL == (srf = srf_open(fname, "r"))) {
+	perror(fname);
+	return -1;
+    }
+
+    /* Read the index header */
+    if (0 != srf_read_index_hdr(srf, &hdr, 0)) {
+	srf_destroy(srf, 1);
+	return list_file(fname, opts);
+    }
+    ipos = ftello(srf->fp);
+
+    /* Compute the remaining size of the index and divide by item_sz */
+    if (hdr.dbh_pos_stored_sep)
+	item_sz += 4;
+    skip = hdr.index_hdr_sz 
+	 + hdr.n_container * 8
+	 + hdr.n_data_block_hdr * 8
+	 + hdr.n_buckets * 8;
+
+    srf_destroy(srf, 1);
+
+    return (hdr.size - skip - 16/* footer*/) / item_sz;
+}
+
+void usage(int error) {
+    printf("Usage: srf_list [options] srf_file ...\n");
+    printf("Options:  -c\tCount only - do not list filenames\n");
+    printf("          -v\tVerbose - gives summary data per file too\n");
+    printf("          -l\tList in long format. Lines contain:\n");
+    printf("            \t    name position body-size header-size\n");
+
+    exit(error);
+}
+
+/*
+ * Lists the contents of a .hash file
+ */
+int main(int argc, char **argv) {
+    opts opts;
+    int i, c;
+    int64_t count = 0;
+
+    opts.long_format = 0;
+    opts.count_only = 0;
+    opts.verbose = 0;
+
+    while ((c = getopt(argc, argv, "lcvh")) != -1) {
+	switch (c) {
+	case 'l':
+	    opts.long_format = 1;
+	    break;
+
+	case 'c':
+	    opts.count_only = 1;
+	    break;
+
+	case 'v':
+	    opts.verbose = 1;
+	    break;
+
+	case 'h':
+	    usage(0);
+
+	default:
+	    usage(1);
+	}
+    }
+
+    for (i = optind; i < argc; i++) {
+	int64_t c;
+
+	if (opts.count_only)
+	    c = count_file(argv[i], &opts);
+	else
+	    c = list_file(argv[i], &opts);
+
+	if (c < 0)
+	    return 1;
+
+	if (opts.verbose)
+	    printf("%s: %d sequences\n", argv[i], c);
+	count += c;
+    }
+    
+    if (opts.count_only)
+	printf("%"PRId64"\n", count);
+
+    return 0;
+}