X-Git-Url: http://woldlab.caltech.edu/gitweb/?p=pysam.git;a=blobdiff_plain;f=samtools%2Fbam_stat.c;fp=samtools%2Fbam_stat.c;h=0000000000000000000000000000000000000000;hp=ea9deee9d712c71bfd51f7574a5cae055a2c2ace;hb=d02fe5283ed7a93a2f76a5d6dc6e37b40c11b9b1;hpb=d828f9c9aa78e3d1687265b52de841f3f3852089

diff --git a/samtools/bam_stat.c b/samtools/bam_stat.c
deleted file mode 100644
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;
-}