X-Git-Url: http://woldlab.caltech.edu/gitweb/?p=pysam.git;a=blobdiff_plain;f=samtools%2Fbam_stat.c.pysam.c;fp=samtools%2Fbam_stat.c.pysam.c;h=4751782ce8e526c28adf00e85bbe1557e299348d;hp=0000000000000000000000000000000000000000;hb=d02fe5283ed7a93a2f76a5d6dc6e37b40c11b9b1;hpb=d828f9c9aa78e3d1687265b52de841f3f3852089

diff --git a/samtools/bam_stat.c.pysam.c b/samtools/bam_stat.c.pysam.c
new file mode 100644
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;
+}