diff srf2fastq/io_lib-1.12.2/progs/trace_dump.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/trace_dump.c	Tue Jun 07 17:48:05 2011 -0400
@@ -0,0 +1,99 @@
+/*
+ * Copyright (c) Medical Research Council 2002. All rights reserved.
+ *
+ * Permission to use, copy, modify and distribute this software and its
+ * documentation for any purpose is hereby granted without fee, provided that
+ * this copyright and notice appears in all copies.
+ *
+ * This file was written by James Bonfield, Simon Dear, Rodger Staden,
+ * Mark Jordan as part of the Staden Package at the MRC Laboratory of
+ * Molecular Biology, Hills Road, Cambridge, CB2 2QH, United Kingdom.
+ *
+ * MRC disclaims all warranties with regard to this software.
+ */
+
+#include <stdio.h>
+#include <io_lib/Read.h>
+
+int main(int argc, char **argv)
+{
+    Read* read;
+    int i;
+
+    if (argc != 2) {
+    fprintf(stderr, "Usage: trace_dump <trace file>\n");
+    return 1;
+    }
+
+
+    read = read_reading( argv[1], TT_ANY );
+
+
+    if (read == NULL) {
+    fprintf(stderr, "Tracedump was unable to open file %s\n", argv[1] );
+    return 1;
+    }
+
+    printf("[Trace]\n");
+    printf("%s\n", read->trace_name );
+
+    printf("\n[Header]\n");
+    printf("%d\t\t# format\n",          read->format);
+    printf("%d\t\t# NPoints\n",         read->NPoints);
+    printf("%d\t\t# NBases\n",          read->NBases);
+    printf("%d\t\t# NFlows\n",          read->nflows);
+    printf("%d\t\t# maxTraceVal\n",     (int)read->maxTraceVal-read->baseline);
+    printf("%d\t\t# baseline\n",        read->baseline);
+    printf("%d\t\t# leftCutoff\n",      read->leftCutoff);
+    printf("%d\t\t# rightCutoff\n",     read->rightCutoff);
+
+    puts("\n[Bases]");
+    for (i = 0; i < read->NBases; i++) {
+    printf("%c %05d %+03d %+03d %+03d %+03d #%3d\n",
+           read->base[i],
+           read->basePos ? read->basePos[i] : 0,
+           (int)read->prob_A[i],
+           (int)read->prob_C[i],
+           (int)read->prob_G[i],
+           (int)read->prob_T[i],
+           i);
+    }
+
+    if (read->NPoints) {
+	puts("\n[A_Trace]");
+	for(i = 0; i < read->NPoints; i++)
+	    printf("%d\t#%5d\n", (int)read->traceA[i] - read->baseline, i);
+
+	puts("\n[C_Trace]");
+	for(i = 0; i < read->NPoints; i++)
+	    printf("%d\t#%5d\n", (int)read->traceC[i] - read->baseline, i);
+
+	puts("\n[G_Trace]");
+	for(i = 0; i < read->NPoints; i++)
+	    printf("%d\t#%5d\n", (int)read->traceG[i] - read->baseline, i);
+
+	puts("\n[T_Trace]");
+	for(i = 0; i < read->NPoints; i++)
+	    printf("%d\t#%5d\n", (int)read->traceT[i] - read->baseline, i);
+    }
+
+    if (read->flow_order) {
+	puts("\n[Flows]");
+	for (i = 0; i < read->nflows; i++) {
+	    printf("%c %5.2f  %u\t#%5d\n",
+		   read->flow_order[i],
+		   read->flow ? read->flow[i] : 0,
+		   read->flow_raw ? read->flow_raw[i] : 0,
+		   i);
+	}
+    }
+
+    if (read->info) {
+	puts("\n[Info]");
+	printf("%s\n", read->info);
+    }
+
+    read_deallocate(read);
+
+    return 0;
+}