Mercurial > repos > dawe > srf2fastq
annotate 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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0
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Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
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1 /* |
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2 * Copyright (c) Medical Research Council 2002. All rights reserved. |
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3 * |
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4 * Permission to use, copy, modify and distribute this software and its |
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5 * documentation for any purpose is hereby granted without fee, provided that |
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6 * this copyright and notice appears in all copies. |
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7 * |
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8 * This file was written by James Bonfield, Simon Dear, Rodger Staden, |
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9 * Mark Jordan as part of the Staden Package at the MRC Laboratory of |
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10 * Molecular Biology, Hills Road, Cambridge, CB2 2QH, United Kingdom. |
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11 * |
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12 * MRC disclaims all warranties with regard to this software. |
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13 */ |
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14 |
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15 #include <stdio.h> |
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16 #include <io_lib/Read.h> |
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17 |
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18 int main(int argc, char **argv) |
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19 { |
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20 Read* read; |
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21 int i; |
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22 |
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23 if (argc != 2) { |
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24 fprintf(stderr, "Usage: trace_dump <trace file>\n"); |
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25 return 1; |
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26 } |
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27 |
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28 |
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29 read = read_reading( argv[1], TT_ANY ); |
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30 |
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31 |
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32 if (read == NULL) { |
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33 fprintf(stderr, "Tracedump was unable to open file %s\n", argv[1] ); |
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34 return 1; |
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35 } |
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36 |
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37 printf("[Trace]\n"); |
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38 printf("%s\n", read->trace_name ); |
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39 |
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40 printf("\n[Header]\n"); |
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41 printf("%d\t\t# format\n", read->format); |
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42 printf("%d\t\t# NPoints\n", read->NPoints); |
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43 printf("%d\t\t# NBases\n", read->NBases); |
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44 printf("%d\t\t# NFlows\n", read->nflows); |
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45 printf("%d\t\t# maxTraceVal\n", (int)read->maxTraceVal-read->baseline); |
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46 printf("%d\t\t# baseline\n", read->baseline); |
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47 printf("%d\t\t# leftCutoff\n", read->leftCutoff); |
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48 printf("%d\t\t# rightCutoff\n", read->rightCutoff); |
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49 |
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50 puts("\n[Bases]"); |
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51 for (i = 0; i < read->NBases; i++) { |
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52 printf("%c %05d %+03d %+03d %+03d %+03d #%3d\n", |
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53 read->base[i], |
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54 read->basePos ? read->basePos[i] : 0, |
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55 (int)read->prob_A[i], |
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56 (int)read->prob_C[i], |
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57 (int)read->prob_G[i], |
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58 (int)read->prob_T[i], |
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59 i); |
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60 } |
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61 |
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62 if (read->NPoints) { |
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63 puts("\n[A_Trace]"); |
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64 for(i = 0; i < read->NPoints; i++) |
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65 printf("%d\t#%5d\n", (int)read->traceA[i] - read->baseline, i); |
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66 |
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67 puts("\n[C_Trace]"); |
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68 for(i = 0; i < read->NPoints; i++) |
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69 printf("%d\t#%5d\n", (int)read->traceC[i] - read->baseline, i); |
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70 |
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71 puts("\n[G_Trace]"); |
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72 for(i = 0; i < read->NPoints; i++) |
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73 printf("%d\t#%5d\n", (int)read->traceG[i] - read->baseline, i); |
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74 |
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75 puts("\n[T_Trace]"); |
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76 for(i = 0; i < read->NPoints; i++) |
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77 printf("%d\t#%5d\n", (int)read->traceT[i] - read->baseline, i); |
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78 } |
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79 |
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80 if (read->flow_order) { |
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81 puts("\n[Flows]"); |
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82 for (i = 0; i < read->nflows; i++) { |
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83 printf("%c %5.2f %u\t#%5d\n", |
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84 read->flow_order[i], |
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85 read->flow ? read->flow[i] : 0, |
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86 read->flow_raw ? read->flow_raw[i] : 0, |
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87 i); |
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88 } |
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89 } |
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90 |
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91 if (read->info) { |
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92 puts("\n[Info]"); |
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93 printf("%s\n", read->info); |
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94 } |
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95 |
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96 read_deallocate(read); |
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97 |
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98 return 0; |
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99 } |