Imported Upstream version 0.5

[pysam.git] / samtools / bam_stat.c.pysam.c

diff --git a/samtools/bam_stat.c.pysam.c b/samtools/bam_stat.c.pysam.c
new file mode 100644 (file)
index 0000000..4751782
--- /dev/null
+++ b/samtools/bam_stat.c.pysam.c
@@ -0,0 +1,79 @@
+#include "pysam.h"
+
+#include <unistd.h>
+#include <assert.h>
+#include "bam.h"
+
+typedef struct {
+       long long n_reads[2], n_mapped[2], n_pair_all[2], n_pair_map[2], n_pair_good[2];
+       long long n_sgltn[2], n_read1[2], n_read2[2];
+       long long n_dup[2];
+       long long n_diffchr[2], n_diffhigh[2];
+} bam_flagstat_t;
+
+#define flagstat_loop(s, c) do {                                                                               \
+               int w = ((c)->flag & BAM_FQCFAIL)? 1 : 0;                                               \
+               ++(s)->n_reads[w];                                                                                              \
+               if ((c)->flag & BAM_FPAIRED) {                                                                  \
+                       ++(s)->n_pair_all[w];                                                                           \
+                       if ((c)->flag & BAM_FPROPER_PAIR) ++(s)->n_pair_good[w];        \
+                       if ((c)->flag & BAM_FREAD1) ++(s)->n_read1[w];                          \
+                       if ((c)->flag & BAM_FREAD2) ++(s)->n_read2[w];                          \
+                       if (((c)->flag & BAM_FMUNMAP) && !((c)->flag & BAM_FUNMAP)) ++(s)->n_sgltn[w];  \
+                       if (!((c)->flag & BAM_FUNMAP) && !((c)->flag & BAM_FMUNMAP)) { \
+                               ++(s)->n_pair_map[w];                                                                   \
+                               if ((c)->mtid != (c)->tid) {                                                    \
+                                       ++(s)->n_diffchr[w];                                                            \
+                                       if ((c)->qual >= 5) ++(s)->n_diffhigh[w];                       \
+                               }                                                                                                               \
+                       }                                                                                                                       \
+               }                                                                                                                               \
+               if (!((c)->flag & BAM_FUNMAP)) ++(s)->n_mapped[w];                              \
+               if ((c)->flag & BAM_FDUP) ++(s)->n_dup[w];                                              \
+       } 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(pysamerr, "[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(pysamerr, "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 + %lld in total (QC-passed reads + QC-failed reads)\n", s->n_reads[0], s->n_reads[1]);
+       printf("%lld + %lld duplicates\n", s->n_dup[0], s->n_dup[1]);
+       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);
+       printf("%lld + %lld paired in sequencing\n", s->n_pair_all[0], s->n_pair_all[1]);
+       printf("%lld + %lld read1\n", s->n_read1[0], s->n_read1[1]);
+       printf("%lld + %lld read2\n", s->n_read2[0], s->n_read2[1]);
+       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);
+       printf("%lld + %lld with itself and mate mapped\n", s->n_pair_map[0], s->n_pair_map[1]);
+       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);
+       printf("%lld + %lld with mate mapped to a different chr\n", s->n_diffchr[0], s->n_diffchr[1]);
+       printf("%lld + %lld with mate mapped to a different chr (mapQ>=5)\n", s->n_diffhigh[0], s->n_diffhigh[1]);
+       free(s);
+       bam_header_destroy(header);
+       bam_close(fp);
+       return 0;
+}