diff srf2fastq/io_lib-1.12.2/progs/hash_extract.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/hash_extract.c	Tue Jun 07 17:48:05 2011 -0400
@@ -0,0 +1,89 @@
+#include <stdio.h>
+#include <string.h>
+#include <stdlib.h>
+#include <fcntl.h>
+#include <io_lib/hash_table.h>
+
+/*
+ * Copies a single named file to stdout.
+ * Returns 0 on success
+ *         1 on failure
+ */
+int extract(HashFile *hf, char *file) {
+    size_t len;
+    char *data;
+
+    if (data = HashFileExtract(hf, file, &len)) {
+	fwrite(data, len, 1, stdout);
+	free(data);
+	return 0;
+    }
+    return 1;
+}
+
+int main(int argc, char **argv) {
+    char *fofn = NULL;
+    char *hash;
+    HashFile *hf;
+    int ret = 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, "-I") == 0) {
+	    argv++;
+	    fofn = *argv;
+	    argc--;
+	}
+    }
+
+    if (argc < 2 && !fofn) {
+	fprintf(stderr, "Usage: hash_extract [-I fofn] hashfile [name ...]\n");
+	return 1;
+    }
+    hash = argv[0];
+    argc--;
+    argv++;
+
+    if (NULL == (hf = HashFileOpen(hash))) {
+	perror(hash);
+	return 1;
+    }
+
+    if (fofn) {
+	FILE *fofnfp;
+	char file[256];
+
+	if (strcmp(fofn, "-") == 0) {
+	    fofnfp = stdin;
+	} else {
+	    if (NULL == (fofnfp = fopen(fofn, "r"))) {
+		perror(fofn);
+		return 1;
+	    }
+	}
+
+	while (fgets(file, 255, fofnfp)) {
+	    char *c;
+	    if (c = strchr(file, '\n'))
+		*c = 0;
+
+	    ret |= extract(hf, file);
+	}
+
+	fclose(fofnfp);
+    }
+
+#ifdef _WIN32
+    _setmode(_fileno(stdout), _O_BINARY);
+#endif
+    for (; argc; argc--, argv++) {
+	ret |= extract(hf, *argv);
+    }
+
+    HashFileDestroy(hf);
+
+    return ret;
+}