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1 #include <unistd.h>
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2 #include <assert.h>
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3 #include "bam.h"
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4
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5 typedef struct {
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6 long long n_reads[2], n_mapped[2], n_pair_all[2], n_pair_map[2], n_pair_good[2];
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7 long long n_sgltn[2], n_read1[2], n_read2[2];
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8 long long n_dup[2];
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9 long long n_diffchr[2], n_diffhigh[2];
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10 } bam_flagstat_t;
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11
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12 #define flagstat_loop(s, c) do { \
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13 int w = ((c)->flag & BAM_FQCFAIL)? 1 : 0; \
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14 ++(s)->n_reads[w]; \
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15 if ((c)->flag & BAM_FPAIRED) { \
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16 ++(s)->n_pair_all[w]; \
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17 if ((c)->flag & BAM_FPROPER_PAIR) ++(s)->n_pair_good[w]; \
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18 if ((c)->flag & BAM_FREAD1) ++(s)->n_read1[w]; \
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19 if ((c)->flag & BAM_FREAD2) ++(s)->n_read2[w]; \
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20 if (((c)->flag & BAM_FMUNMAP) && !((c)->flag & BAM_FUNMAP)) ++(s)->n_sgltn[w]; \
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21 if (!((c)->flag & BAM_FUNMAP) && !((c)->flag & BAM_FMUNMAP)) { \
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22 ++(s)->n_pair_map[w]; \
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23 if ((c)->mtid != (c)->tid) { \
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24 ++(s)->n_diffchr[w]; \
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25 if ((c)->qual >= 5) ++(s)->n_diffhigh[w]; \
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26 } \
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27 } \
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28 } \
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29 if (!((c)->flag & BAM_FUNMAP)) ++(s)->n_mapped[w]; \
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30 if ((c)->flag & BAM_FDUP) ++(s)->n_dup[w]; \
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31 } while (0)
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32
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33 bam_flagstat_t *bam_flagstat_core(bamFile fp)
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34 {
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35 bam_flagstat_t *s;
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36 bam1_t *b;
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37 bam1_core_t *c;
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38 int ret;
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39 s = (bam_flagstat_t*)calloc(1, sizeof(bam_flagstat_t));
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40 b = bam_init1();
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41 c = &b->core;
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42 while ((ret = bam_read1(fp, b)) >= 0)
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43 flagstat_loop(s, c);
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44 bam_destroy1(b);
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45 if (ret != -1)
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46 fprintf(stderr, "[bam_flagstat_core] Truncated file? Continue anyway.\n");
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47 return s;
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48 }
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49 int bam_flagstat(int argc, char *argv[])
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50 {
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51 bamFile fp;
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52 bam_header_t *header;
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53 bam_flagstat_t *s;
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54 if (argc == optind) {
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55 fprintf(stderr, "Usage: samtools flagstat <in.bam>\n");
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56 return 1;
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57 }
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58 fp = strcmp(argv[optind], "-")? bam_open(argv[optind], "r") : bam_dopen(fileno(stdin), "r");
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59 assert(fp);
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60 header = bam_header_read(fp);
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61 s = bam_flagstat_core(fp);
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62 printf("%lld + %lld in total (QC-passed reads + QC-failed reads)\n", s->n_reads[0], s->n_reads[1]);
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63 printf("%lld + %lld duplicates\n", s->n_dup[0], s->n_dup[1]);
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64 printf("%lld + %lld mapped (%.2f%%:%.2f%%)\n", s->n_mapped[0], s->n_mapped[1], (float)s->n_mapped[0] / s->n_reads[0] * 100.0, (float)s->n_mapped[1] / s->n_reads[1] * 100.0);
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65 printf("%lld + %lld paired in sequencing\n", s->n_pair_all[0], s->n_pair_all[1]);
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66 printf("%lld + %lld read1\n", s->n_read1[0], s->n_read1[1]);
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67 printf("%lld + %lld read2\n", s->n_read2[0], s->n_read2[1]);
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68 printf("%lld + %lld properly paired (%.2f%%:%.2f%%)\n", s->n_pair_good[0], s->n_pair_good[1], (float)s->n_pair_good[0] / s->n_pair_all[0] * 100.0, (float)s->n_pair_good[1] / s->n_pair_all[1] * 100.0);
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69 printf("%lld + %lld with itself and mate mapped\n", s->n_pair_map[0], s->n_pair_map[1]);
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70 printf("%lld + %lld singletons (%.2f%%:%.2f%%)\n", s->n_sgltn[0], s->n_sgltn[1], (float)s->n_sgltn[0] / s->n_pair_all[0] * 100.0, (float)s->n_sgltn[1] / s->n_pair_all[1] * 100.0);
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71 printf("%lld + %lld with mate mapped to a different chr\n", s->n_diffchr[0], s->n_diffchr[1]);
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72 printf("%lld + %lld with mate mapped to a different chr (mapQ>=5)\n", s->n_diffhigh[0], s->n_diffhigh[1]);
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73 free(s);
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74 bam_header_destroy(header);
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75 bam_close(fp);
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76 return 0;
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77 }
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