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6
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1 #ifndef MAQMAP_H_
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2 #define MAQMAP_H_
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3
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4 #ifdef MAQ_LONGREADS
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5 # define MAX_READLEN 128
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6 #else
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7 # define MAX_READLEN 64
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8 #endif
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9
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10 #define MAX_NAMELEN 36
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11 #define MAQMAP_FORMAT_OLD 0
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12 #define MAQMAP_FORMAT_NEW -1
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13
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14 #define PAIRFLAG_FF 0x01
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15 #define PAIRFLAG_FR 0x02
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16 #define PAIRFLAG_RF 0x04
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17 #define PAIRFLAG_RR 0x08
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18 #define PAIRFLAG_PAIRED 0x10
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19 #define PAIRFLAG_DIFFCHR 0x20
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20 #define PAIRFLAG_NOMATCH 0x40
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21 #define PAIRFLAG_SW 0x80
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22
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23 #include <string.h>
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24 #include <zlib.h>
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25 #include "const.h"
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26
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27 /*
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28 name: read name
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29 size: the length of the read
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30 seq: read sequence (see also below)
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31 seq[MAX_READLEN-1]: single end mapping quality (equals to map_qual if not paired)
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32 map_qual: the final mapping quality
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33 alt_qual: the lower quality of the two ends (equals to map_qual if not paired)
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34 flag: status of the pair
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35 dist: offset of the mate (zero if not paired)
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36 info1: mismatches in the 24bp (higher 4 bits) and mismatches (lower 4 bits)
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37 info2: sum of errors of the best hit
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38 c[2]: count of all 0- and 1-mismatch hits on the reference
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39 */
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40 typedef struct
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41 {
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42 bit8_t seq[MAX_READLEN]; /* the last base is the single-end mapping quality. */
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43 bit8_t size, map_qual, info1, info2, c[2], flag, alt_qual;
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44 bit32_t seqid, pos;
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45 int dist;
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46 char name[MAX_NAMELEN];
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47 } maqmap1_t;
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48
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49 typedef struct
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50 {
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51 int format, n_ref;
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52 char **ref_name;
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53 bit64_t n_mapped_reads;
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54 maqmap1_t *mapped_reads;
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55 } maqmap_t;
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56
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57 #define maqmap_read1(fp, m1) gzread((fp), (m1), sizeof(maqmap1_t))
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58
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59 #ifdef __cplusplus
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60 extern "C" {
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61 #endif
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62 maqmap_t *maq_new_maqmap();
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63 void maq_delete_maqmap(maqmap_t *mm);
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64 void maqmap_write_header(gzFile fp, const maqmap_t *mm);
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65 maqmap_t *maqmap_read_header(gzFile fp);
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66 #ifdef __cplusplus
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67 }
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68 #endif
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69
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70 #endif
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