Mercurial > repos > dawe > srf2fastq
comparison 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
author | dawe |
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date | Tue, 07 Jun 2011 17:48:05 -0400 |
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-1:000000000000 | 0:d901c9f41a6a |
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1 /* | |
2 * Copyright (c) Medical Research Council 2002. All rights reserved. | |
3 * | |
4 * Permission to use, copy, modify and distribute this software and its | |
5 * documentation for any purpose is hereby granted without fee, provided that | |
6 * this copyright and notice appears in all copies. | |
7 * | |
8 * This file was written by James Bonfield, Simon Dear, Rodger Staden, | |
9 * Mark Jordan as part of the Staden Package at the MRC Laboratory of | |
10 * Molecular Biology, Hills Road, Cambridge, CB2 2QH, United Kingdom. | |
11 * | |
12 * MRC disclaims all warranties with regard to this software. | |
13 */ | |
14 | |
15 #include <stdio.h> | |
16 #include <io_lib/Read.h> | |
17 | |
18 int main(int argc, char **argv) | |
19 { | |
20 Read* read; | |
21 int i; | |
22 | |
23 if (argc != 2) { | |
24 fprintf(stderr, "Usage: trace_dump <trace file>\n"); | |
25 return 1; | |
26 } | |
27 | |
28 | |
29 read = read_reading( argv[1], TT_ANY ); | |
30 | |
31 | |
32 if (read == NULL) { | |
33 fprintf(stderr, "Tracedump was unable to open file %s\n", argv[1] ); | |
34 return 1; | |
35 } | |
36 | |
37 printf("[Trace]\n"); | |
38 printf("%s\n", read->trace_name ); | |
39 | |
40 printf("\n[Header]\n"); | |
41 printf("%d\t\t# format\n", read->format); | |
42 printf("%d\t\t# NPoints\n", read->NPoints); | |
43 printf("%d\t\t# NBases\n", read->NBases); | |
44 printf("%d\t\t# NFlows\n", read->nflows); | |
45 printf("%d\t\t# maxTraceVal\n", (int)read->maxTraceVal-read->baseline); | |
46 printf("%d\t\t# baseline\n", read->baseline); | |
47 printf("%d\t\t# leftCutoff\n", read->leftCutoff); | |
48 printf("%d\t\t# rightCutoff\n", read->rightCutoff); | |
49 | |
50 puts("\n[Bases]"); | |
51 for (i = 0; i < read->NBases; i++) { | |
52 printf("%c %05d %+03d %+03d %+03d %+03d #%3d\n", | |
53 read->base[i], | |
54 read->basePos ? read->basePos[i] : 0, | |
55 (int)read->prob_A[i], | |
56 (int)read->prob_C[i], | |
57 (int)read->prob_G[i], | |
58 (int)read->prob_T[i], | |
59 i); | |
60 } | |
61 | |
62 if (read->NPoints) { | |
63 puts("\n[A_Trace]"); | |
64 for(i = 0; i < read->NPoints; i++) | |
65 printf("%d\t#%5d\n", (int)read->traceA[i] - read->baseline, i); | |
66 | |
67 puts("\n[C_Trace]"); | |
68 for(i = 0; i < read->NPoints; i++) | |
69 printf("%d\t#%5d\n", (int)read->traceC[i] - read->baseline, i); | |
70 | |
71 puts("\n[G_Trace]"); | |
72 for(i = 0; i < read->NPoints; i++) | |
73 printf("%d\t#%5d\n", (int)read->traceG[i] - read->baseline, i); | |
74 | |
75 puts("\n[T_Trace]"); | |
76 for(i = 0; i < read->NPoints; i++) | |
77 printf("%d\t#%5d\n", (int)read->traceT[i] - read->baseline, i); | |
78 } | |
79 | |
80 if (read->flow_order) { | |
81 puts("\n[Flows]"); | |
82 for (i = 0; i < read->nflows; i++) { | |
83 printf("%c %5.2f %u\t#%5d\n", | |
84 read->flow_order[i], | |
85 read->flow ? read->flow[i] : 0, | |
86 read->flow_raw ? read->flow_raw[i] : 0, | |
87 i); | |
88 } | |
89 } | |
90 | |
91 if (read->info) { | |
92 puts("\n[Info]"); | |
93 printf("%s\n", read->info); | |
94 } | |
95 | |
96 read_deallocate(read); | |
97 | |
98 return 0; | |
99 } |