Mercurial > repos > dawe > srf2fastq
annotate srf2fastq/io_lib-1.12.2/progs/append_sff.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
d901c9f41a6a
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 * Concatenates multiple SFF files together. It also strips out any indexing |
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3 * so this will need to be added again afterwards. |
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4 * |
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5 * The first argument is the archive to append to. All subsequent arguments |
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6 * are the archives to append to the first argument. |
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7 */ |
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8 |
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9 #include <stdio.h> |
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10 #include <string.h> |
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11 #include <errno.h> |
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12 #include <stdlib.h> |
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13 #include <io_lib/sff.h> |
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14 #include <io_lib/os.h> |
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15 |
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16 #define BSIZE 1024*1024 |
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17 |
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18 int main(int argc, char **argv) { |
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19 int i; |
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20 FILE *fpin, *fpout; |
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21 unsigned char *block; |
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22 unsigned char chdr[31]; |
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23 sff_common_header *ch; |
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24 |
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25 block = (unsigned char *)malloc(BSIZE); |
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26 |
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27 if (argc < 3) { |
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28 fprintf(stderr, "Usage: append_sff sff_file add_me.sff ...\n"); |
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29 return 1; |
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30 } |
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31 |
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32 /* Open and decode the common header of the archive we'll append to */ |
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33 if (NULL == (fpout = fopen(argv[1], "rb+"))) { |
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34 perror(argv[1]); |
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35 return 1; |
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36 } |
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37 |
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38 if (31 != fread(chdr, 1, 31, fpout)) { |
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39 fprintf(stderr, "Couldn't read common header\n"); |
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40 return 1; |
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41 } |
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42 ch = decode_sff_common_header(chdr); |
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43 |
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44 /* |
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45 * Jump to the end of the archive or the start of the index. |
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46 * NB: If the index is not at the end we cannot use a simple append |
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47 * method. |
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48 */ |
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49 fseek(fpout, 0, SEEK_END); |
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50 if (ch->index_len) { |
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51 if (ch->index_offset + ch->index_len != ftell(fpout)) { |
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52 fprintf(stderr, "Index is not at the end of file => cannot append\n"); |
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53 return 1; |
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54 } |
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55 fseek(fpout, ch->index_offset, SEEK_SET); |
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56 } |
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57 |
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58 /* Iterate around other archives, appending to the first one */ |
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59 for (i = 2; i < argc; i++) { |
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60 sff_common_header *h; |
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61 uint64_t pos; |
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62 size_t len; |
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63 char *sff = argv[i]; |
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64 int skipped; |
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65 |
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66 printf("Copying %s\n", sff); |
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67 |
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68 if (NULL == (fpin = fopen(sff, "rb"))) { |
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69 perror(sff); |
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70 return 1; |
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71 } |
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72 |
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73 if (31 != fread(chdr, 1, 31, fpin)) { |
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74 fprintf(stderr, "Couldn't read common header\n"); |
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75 return 1; |
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76 } |
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77 |
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78 h = decode_sff_common_header(chdr); |
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79 |
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80 /* Check if headers are compatible */ |
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81 if (ch->flow_len != h->flow_len || |
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82 ch->key_len != h->key_len || |
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83 ch->flowgram_format != h->flowgram_format) |
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84 fprintf(stderr, "*** Error: incompatible SFF headers ***\n"); |
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85 fseek(fpin, h->header_len - 31, SEEK_CUR); |
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86 ch->nreads += h->nreads; |
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87 |
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88 /* Copy all data from fpin to fpout, skipping index if present */ |
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89 skipped = h->index_len ? 0 : 1; |
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90 for (pos = ftell(fpin); ; pos += len) { |
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91 len = BSIZE; |
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92 if (!skipped) { |
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93 if (pos == h->index_offset) { |
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94 fseek(fpin, h->index_len, SEEK_CUR); |
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95 pos += h->index_len; |
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96 skipped = 1; |
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97 } else if (pos + BSIZE > h->index_offset) { |
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98 len = h->index_offset - pos; |
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99 } |
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100 } |
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101 if (0 == (len = fread(block, 1, len, fpin))) |
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102 break; |
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103 fwrite(block, 1, len, fpout); |
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104 } |
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105 |
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106 free_sff_common_header(h); |
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107 fclose(fpin); |
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108 } |
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109 |
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110 /* Seek back and update the header with the new nreads */ |
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111 fseek(fpout, 0, SEEK_SET); |
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112 fread(chdr, 1, 31, fpout); |
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113 *(uint64_t *)(chdr+8) = be_int8(0); |
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114 *(uint32_t *)(chdr+16) = be_int4(0); |
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115 *(uint32_t *)(chdr+20) = be_int4(ch->nreads); |
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116 fseek(fpout, 0, SEEK_SET); |
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117 fwrite(chdr, 1, 31, fpout); |
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118 fclose(fpout); |
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119 |
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120 free_sff_common_header(ch); |
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121 free(block); |
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122 |
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123 return 0; |
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124 } |