Mercurial > repos > dawe > srf2fastq
annotate srf2fastq/io_lib-1.12.2/io_lib/sff.h @ 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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Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
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1 #ifndef _SFF_H_ |
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2 #define _SFF_H_ |
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3 |
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4 #include "io_lib/Read.h" |
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5 #include "io_lib/os.h" |
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6 #include "io_lib/mFILE.h" |
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7 |
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8 #ifdef __cplusplus |
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9 extern "C" { |
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10 #endif |
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11 |
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12 /* |
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13 * This mirrors the order that the SFF header has on disc. We have one of |
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14 * these only. |
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15 * |
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16 * The flow and key are variable length fields as defined by flow_len |
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17 * and key_len. |
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18 * The on-disc structure is then also padded out with zeros to the 8-byte |
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19 * word boundary. |
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20 */ |
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21 typedef struct { |
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22 uint32_t magic; |
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23 char version[4]; |
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24 uint64_t index_offset; |
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25 uint32_t index_len; |
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26 uint32_t nreads; |
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27 uint16_t header_len; |
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28 uint16_t key_len; |
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29 uint16_t flow_len; |
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30 uint8_t flowgram_format; |
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31 char *flow; |
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32 char *key; |
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33 } sff_common_header; |
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34 |
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35 #define SFF_MAGIC 0x2e736666 /* ".sff" */ |
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36 #define SFF_VERSION "\0\0\0\1" |
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37 |
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38 /* |
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39 * We have one read_header per "reading" in the SFF archive. |
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40 * It too is padded to an 8-byte boundary. |
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41 */ |
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42 typedef struct { |
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43 uint16_t header_len; |
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44 uint16_t name_len; |
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45 uint32_t nbases; |
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46 uint16_t clip_qual_left; |
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47 uint16_t clip_qual_right; |
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48 uint16_t clip_adapter_left; |
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49 uint16_t clip_adapter_right; |
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50 char *name; |
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51 } sff_read_header; |
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52 |
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53 /* |
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54 * We have one read_data section per reading, following the read_header. |
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55 * It is padded to an 8-byte boundary. |
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56 */ |
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57 typedef struct { |
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58 uint16_t *flowgram; /* x 100.0 */ |
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59 uint8_t *flow_index; /* relative to last */ |
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60 char *bases; |
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61 uint8_t *quality; |
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62 } sff_read_data; |
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63 |
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64 |
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65 /* |
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66 * Low level functions to decode SFF internals |
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67 */ |
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68 sff_common_header *decode_sff_common_header(unsigned char *buf); |
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69 sff_common_header *read_sff_common_header(mFILE *mf); |
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70 void free_sff_common_header(sff_common_header *h); |
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71 sff_read_header *decode_sff_read_header(unsigned char *buf); |
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72 void free_sff_read_header(sff_read_header *h); |
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73 sff_read_header *read_sff_read_header(mFILE *mf); |
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74 void free_sff_read_data(sff_read_data *d); |
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75 sff_read_data *read_sff_read_data(mFILE *mf, int nflows, int nbases); |
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76 |
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77 |
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78 /* |
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79 * Loads the first SFF sequence from an SFF container and returns as a Read. |
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80 */ |
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81 Read *mfread_sff(mFILE *mf); |
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82 |
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83 #ifdef __cplusplus |
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84 } |
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85 #endif |
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86 |
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87 #endif /* _SFF_H_ */ |