X-Git-Url: http://woldlab.caltech.edu/gitweb/?p=samtools.git;a=blobdiff_plain;f=bam_stat.c;h=f2de0f19723bbab0f33fd99af33e0c1a91e45fcc;hp=ea9deee9d712c71bfd51f7574a5cae055a2c2ace;hb=5075acdfc387c56ca8411cde3e419e867da9804d;hpb=4a17fa7e1f91b2fe04ad334a63fc2b0d5e859d8a

diff --git a/bam_stat.c b/bam_stat.c
index ea9deee..f2de0f1 100644
--- a/bam_stat.c
+++ b/bam_stat.c
@@ -3,31 +3,31 @@
 #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;
+	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 {										\
-		++(s)->n_reads;													\
+		int w = ((c)->flag & BAM_FQCFAIL)? 1 : 0;	 					\
+		++(s)->n_reads[w];												\
 		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;	\
+			++(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;										\
+				++(s)->n_pair_map[w];									\
 				if ((c)->mtid != (c)->tid) {							\
-					++(s)->n_diffchr;									\
-					if ((c)->qual >= 5) ++(s)->n_diffhigh;				\
+					++(s)->n_diffchr[w];								\
+					if ((c)->qual >= 5) ++(s)->n_diffhigh[w];			\
 				}														\
 			}															\
 		}																\
-		if (!((c)->flag & BAM_FUNMAP)) ++(s)->n_mapped;					\
-		if ((c)->flag & BAM_FQCFAIL) ++(s)->n_qcfail;					\
-		if ((c)->flag & BAM_FDUP) ++(s)->n_dup;							\
+		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)
@@ -59,18 +59,17 @@ int bam_flagstat(int argc, char *argv[])
 	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);
+	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);