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1 #include <stdlib.h>
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2 #include <string.h>
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3 #include "bam.h"
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4
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5 // currently, this function ONLY works if each read has one hit
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6 void bam_mating_core(bamFile in, bamFile out)
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7 {
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8 bam_header_t *header;
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9 bam1_t *b[2];
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10 int curr, has_prev;
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11
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12 header = bam_header_read(in);
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13 bam_header_write(out, header);
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14
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15 b[0] = bam_init1();
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16 b[1] = bam_init1();
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17 curr = 0; has_prev = 0;
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18 while (bam_read1(in, b[curr]) >= 0) {
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19 bam1_t *cur = b[curr], *pre = b[1-curr];
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20 if (has_prev) {
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21 if (strcmp(bam1_qname(cur), bam1_qname(pre)) == 0) { // identical pair name
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22 cur->core.mtid = pre->core.tid; cur->core.mpos = pre->core.pos;
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23 pre->core.mtid = cur->core.tid; pre->core.mpos = cur->core.pos;
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24 if (pre->core.tid == cur->core.tid && !(cur->core.flag&(BAM_FUNMAP|BAM_FMUNMAP))
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25 && !(pre->core.flag&(BAM_FUNMAP|BAM_FMUNMAP)))
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26 {
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27 uint32_t cur5, pre5;
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28 cur5 = (cur->core.flag&BAM_FREVERSE)? bam_calend(&cur->core, bam1_cigar(cur)) : cur->core.pos;
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29 pre5 = (pre->core.flag&BAM_FREVERSE)? bam_calend(&pre->core, bam1_cigar(pre)) : pre->core.pos;
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30 cur->core.isize = pre5 - cur5; pre->core.isize = cur5 - pre5;
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31 } else cur->core.isize = pre->core.isize = 0;
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32 if (pre->core.flag&BAM_FREVERSE) cur->core.flag |= BAM_FMREVERSE;
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33 else cur->core.flag &= ~BAM_FMREVERSE;
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34 if (cur->core.flag&BAM_FREVERSE) pre->core.flag |= BAM_FMREVERSE;
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35 else pre->core.flag &= ~BAM_FMREVERSE;
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36 if (cur->core.flag & BAM_FUNMAP) { pre->core.flag |= BAM_FMUNMAP; pre->core.flag &= ~BAM_FPROPER_PAIR; }
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37 if (pre->core.flag & BAM_FUNMAP) { cur->core.flag |= BAM_FMUNMAP; cur->core.flag &= ~BAM_FPROPER_PAIR; }
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38 bam_write1(out, pre);
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39 bam_write1(out, cur);
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40 has_prev = 0;
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41 } else { // unpaired or singleton
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42 pre->core.mtid = -1; pre->core.mpos = -1; pre->core.isize = 0;
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43 if (pre->core.flag & BAM_FPAIRED) {
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44 pre->core.flag |= BAM_FMUNMAP;
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45 pre->core.flag &= ~BAM_FMREVERSE & ~BAM_FPROPER_PAIR;
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46 }
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47 bam_write1(out, pre);
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48 }
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49 } else has_prev = 1;
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50 curr = 1 - curr;
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51 }
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52 if (has_prev) bam_write1(out, b[1-curr]);
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53 bam_header_destroy(header);
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54 bam_destroy1(b[0]);
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55 bam_destroy1(b[1]);
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56 }
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57
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58 int bam_mating(int argc, char *argv[])
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59 {
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60 bamFile in, out;
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61 if (argc < 3) {
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62 fprintf(stderr, "samtools fixmate <in.nameSrt.bam> <out.nameSrt.bam>\n");
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63 return 1;
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64 }
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65 in = (strcmp(argv[1], "-") == 0)? bam_dopen(fileno(stdin), "r") : bam_open(argv[1], "r");
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66 out = (strcmp(argv[2], "-") == 0)? bam_dopen(fileno(stdout), "w") : bam_open(argv[2], "w");
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67 bam_mating_core(in, out);
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68 bam_close(in); bam_close(out);
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69 return 0;
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70 }
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