Merge commit 'upstream/0.5'

[pysam.git] / samtools / bam_stat.c

diff --git a/samtools/bam_stat.c b/samtools/bam_stat.c
deleted file mode 100644 (file)
index ea9deee..0000000
--- a/samtools/bam_stat.c
+++ /dev/null
@@ -1,78 +0,0 @@
-#include <unistd.h>
-#include <assert.h>
-#include "bam.h"
-
-typedef struct {
-       long long n_reads, n_mapped, n_pair_all, n_pair_map, n_pair_good;
-       long long n_sgltn, n_read1, n_read2;
-       long long n_qcfail, n_dup;
-       long long n_diffchr, n_diffhigh;
-} bam_flagstat_t;
-
-#define flagstat_loop(s, c) do {                                                                               \
-               ++(s)->n_reads;                                                                                                 \
-               if ((c)->flag & BAM_FPAIRED) {                                                                  \
-                       ++(s)->n_pair_all;                                                                                      \
-                       if ((c)->flag & BAM_FPROPER_PAIR) ++(s)->n_pair_good;           \
-                       if ((c)->flag & BAM_FREAD1) ++(s)->n_read1;                                     \
-                       if ((c)->flag & BAM_FREAD2) ++(s)->n_read2;                                     \
-                       if (((c)->flag & BAM_FMUNMAP) && !((c)->flag & BAM_FUNMAP)) ++(s)->n_sgltn;     \
-                       if (!((c)->flag & BAM_FUNMAP) && !((c)->flag & BAM_FMUNMAP)) { \
-                               ++(s)->n_pair_map;                                                                              \
-                               if ((c)->mtid != (c)->tid) {                                                    \
-                                       ++(s)->n_diffchr;                                                                       \
-                                       if ((c)->qual >= 5) ++(s)->n_diffhigh;                          \
-                               }                                                                                                               \
-                       }                                                                                                                       \
-               }                                                                                                                               \
-               if (!((c)->flag & BAM_FUNMAP)) ++(s)->n_mapped;                                 \
-               if ((c)->flag & BAM_FQCFAIL) ++(s)->n_qcfail;                                   \
-               if ((c)->flag & BAM_FDUP) ++(s)->n_dup;                                                 \
-       } while (0)
-
-bam_flagstat_t *bam_flagstat_core(bamFile fp)
-{
-       bam_flagstat_t *s;
-       bam1_t *b;
-       bam1_core_t *c;
-       int ret;
-       s = (bam_flagstat_t*)calloc(1, sizeof(bam_flagstat_t));
-       b = bam_init1();
-       c = &b->core;
-       while ((ret = bam_read1(fp, b)) >= 0)
-               flagstat_loop(s, c);
-       bam_destroy1(b);
-       if (ret != -1)
-               fprintf(stderr, "[bam_flagstat_core] Truncated file? Continue anyway.\n");
-       return s;
-}
-int bam_flagstat(int argc, char *argv[])
-{
-       bamFile fp;
-       bam_header_t *header;
-       bam_flagstat_t *s;
-       if (argc == optind) {
-               fprintf(stderr, "Usage: samtools flagstat <in.bam>\n");
-               return 1;
-       }
-       fp = strcmp(argv[optind], "-")? bam_open(argv[optind], "r") : bam_dopen(fileno(stdin), "r");
-       assert(fp);
-       header = bam_header_read(fp);
-       s = bam_flagstat_core(fp);
-       printf("%lld in total\n", s->n_reads);
-       printf("%lld QC failure\n", s->n_qcfail);
-       printf("%lld duplicates\n", s->n_dup);
-       printf("%lld mapped (%.2f%%)\n", s->n_mapped, (float)s->n_mapped / s->n_reads * 100.0);
-       printf("%lld paired in sequencing\n", s->n_pair_all);
-       printf("%lld read1\n", s->n_read1);
-       printf("%lld read2\n", s->n_read2);
-       printf("%lld properly paired (%.2f%%)\n", s->n_pair_good, (float)s->n_pair_good / s->n_pair_all * 100.0);
-       printf("%lld with itself and mate mapped\n", s->n_pair_map);
-       printf("%lld singletons (%.2f%%)\n", s->n_sgltn, (float)s->n_sgltn / s->n_pair_all * 100.0);
-       printf("%lld with mate mapped to a different chr\n", s->n_diffchr);
-       printf("%lld with mate mapped to a different chr (mapQ>=5)\n", s->n_diffhigh);
-       free(s);
-       bam_header_destroy(header);
-       bam_close(fp);
-       return 0;
-}