diff srf2fastq/io_lib-1.12.2/progs/index_tar.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/index_tar.c	Tue Jun 07 17:48:05 2011 -0400
@@ -0,0 +1,96 @@
+#include <stdio.h>
+#include <string.h>
+#include <errno.h>
+#include <stdlib.h>
+#include <io_lib/tar_format.h>
+
+int main(int argc, char **argv) {
+    int directories = 0;
+    FILE *fp;
+    tar_block blk;
+    char member[256];
+    size_t size, extra;
+    int LongLink = 0;
+    size_t offset = 0;
+    
+    /* process command line arguments of the form -arg */
+    for (argc--, argv++; argc > 0; argc--, argv++) {
+	if (**argv != '-' || strcmp(*argv, "--") == 0)
+	    break;
+
+	if (strcmp(*argv, "-d") == 0)
+	    directories = 1;
+    }
+
+    if (argc != 1) {
+	fprintf(stderr, "Usage: index_tar [-d] tarfile > tarfile.index\n");
+	return 1;
+    }
+
+    /* open the tarfile */
+    if (NULL == (fp = fopen(argv[0], "rb"))) {
+	perror(argv[0]);
+	return 1;
+    }
+
+    while(fread(&blk, sizeof(blk), 1, fp) == 1) {
+	/*
+	 * If a directory is too large to fit in the name (>100) but short
+	 * enough to fit in the prefix the name field will be empty, this is
+	 * not the case for ordinary files where the name field is always
+	 * non-empty
+	 */
+	if (!blk.header.name[0] && !blk.header.prefix[0])
+	    break;
+
+        /* get size of member, rounded to a multiple of TBLOCK */
+	size = strtoul(blk.header.size, NULL, 8);
+        extra = TBLOCK*((size+TBLOCK-1)/TBLOCK) - size;
+
+        /* skip directories unless requested */
+        if (directories || blk.header.typeflag != DIRTYPE || LongLink) {
+
+            /*
+	     * extract member name (prefix + name), unless last member
+	     * was ././@LongLink
+	     */
+            if (LongLink == 0) {
+                (void) strncpy(member, blk.header.prefix, 155);
+	        if (strlen(blk.header.prefix) > 0 && blk.header.name[0])
+		    (void) strcat(member, "/");
+    	        (void) strncat(member, blk.header.name, 100);
+            }
+            
+            /* account for gtar ././@LongLink */
+            if (strcmp(member, "././@LongLink") == 0) {
+                /* still expect filenames to fit into 256 bytes */
+                if (size > 256) {
+                    fread(member, 1, size > 256 ? 256 : size, fp);
+                    fprintf(stderr,"././@LongLink too long size=%ld\n",
+			    (long)size);
+                    fprintf(stderr,"%s...\n", member);
+                    exit(1);
+                }
+                /*
+		 * extract full name of next member then rewind to start
+		 * of header
+		 */
+                fread(member, 1, size > 256 ? 256 : size, fp);
+                fseek(fp, -size, SEEK_CUR);
+                LongLink = 1;
+            } else {
+                /* output offset, member name */
+                printf("%lu %.256s\n", (long)offset, member);
+                LongLink = 0;
+            }
+        }
+
+        /* increment offset */
+        size += extra;
+        fseek(fp, size, SEEK_CUR);
+        offset += sizeof(blk) + size;
+    }
+
+    fclose(fp);
+    return 0;
+}