diff srf2fastq/io_lib-1.12.2/progs/srf_index_hash.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_index_hash.c	Tue Jun 07 17:48:05 2011 -0400
@@ -0,0 +1,144 @@
+/*
+ * This adds a hash table index (".hsh" v1.01 format) to an SRF archive.
+ * It does this either inline on the file itself (provided it doesn't already
+ * have an index) or by producing an external index file.
+ */
+
+/* ---------------------------------------------------------------------- */
+
+#ifdef HAVE_CONFIG_H
+#include "io_lib_config.h"
+#endif
+
+#include <stdio.h>
+#include <string.h>
+#include <errno.h>
+#include <stdlib.h>
+#include <unistd.h>
+#include <sys/types.h>
+#include <io_lib/hash_table.h>
+#include <io_lib/os.h>
+#include <io_lib/array.h>
+#include <io_lib/srf.h>
+
+/* ------------------------------------------------------------------------ */
+void usage(int code) {
+    printf("Usage: srf_index_hash [-c] srf_file\n");
+    printf(" Options:\n");
+    printf("    -c       check an existing index, don't re-index\n");
+    exit(code);
+}
+
+int main(int argc, char **argv) {
+    srf_t *srf;
+    uint64_t pos;
+    char name[512];
+    int i, type;
+    char *archive;
+    int dbh_pos_stored_sep = 0;
+    int check = 0;
+    off_t old_index = 0;
+    srf_index_t *idx;
+    
+    /* Parse args */
+    for (i = 1; i < argc && argv[i][0] == '-'; i++) {
+	if (!strcmp(argv[i], "-")) {
+	    break;
+	} else if (!strcmp(argv[i], "-c")) {
+	    check = 1;
+	} else if (!strcmp(argv[i], "-h")) {
+	    usage(0);
+	} else {
+	    usage(1);
+	}
+    }
+
+    if (argc != (i+1)) {
+      usage(1);
+    }
+
+    archive = argv[i];
+
+    if( check ){
+        srf = srf_open(archive, "rb");
+    } else {
+        srf = srf_open(archive, "r+b");
+    }
+    if (NULL == srf ){
+ 	perror(argv[i]);
+	return 1;
+    }
+    
+    
+    idx = srf_index_create(NULL, NULL, dbh_pos_stored_sep);
+    if (NULL == idx)
+	return 1;
+
+    /* Scan through file gathering the details to index in memory */
+    while ((type = srf_next_block_details(srf, &pos, name)) >= 0) {
+	/* Only want this set if the last block in the file is an index */
+	old_index = 0;
+
+	switch (type) {
+	case SRFB_CONTAINER:
+	    if (srf_index_add_cont_hdr(idx, pos))
+		return 1;
+	    break;
+
+	case SRFB_TRACE_HEADER:
+	    if (srf_index_add_trace_hdr(idx, pos))
+		return 1;
+	    break;
+
+	case SRFB_TRACE_BODY:
+	    if (srf_index_add_trace_body(idx, name, pos))
+		return 1;
+	    break;
+
+	case SRFB_INDEX:
+	    /* An old index */
+	    old_index = pos;
+	    break;
+
+        case SRFB_NULL_INDEX:
+	    old_index = pos;
+            break;
+
+	default:
+	    abort();
+	}
+    }
+
+    /* the type should be -1 (EOF) */
+    if( type != -1 )
+        abort();
+
+    /* are we really at the end of the srf file */
+    pos = ftell(srf->fp);
+    fseek(srf->fp, 0, SEEK_END);
+    if( pos != ftell(srf->fp) ){
+        fprintf(stderr, "srf file is corrupt\n");
+	return 1;
+    }
+    
+    if (check) {
+	srf_index_destroy(idx);
+	srf_destroy(srf, 1);
+	return 0;
+    }
+
+    /* Write out the index */
+    if (old_index)
+	fseeko(srf->fp, old_index, SEEK_SET);
+
+    srf_index_stats(idx, NULL);
+    srf_index_write(srf, idx);
+
+    /* Truncate incase we've somehow overwritten an old longer index */
+    ftruncate(fileno(srf->fp), ftello(srf->fp));
+
+    srf_index_destroy(idx);
+    srf_destroy(srf, 1);
+    
+    return 0;
+}