X-Git-Url: http://woldlab.caltech.edu/gitweb/?p=pysam.git;a=blobdiff_plain;f=samtools%2Fbam_mate.c;fp=samtools%2Fbam_mate.c;h=0000000000000000000000000000000000000000;hp=61f808a26402e9bd1d332f40074b4b3ca1f89dd3;hb=bd0c3067c187d1f718004fb38acc093af8810a02;hpb=1b740fc70684c92a5e2293013217d5a2fd661d8a

diff --git a/samtools/bam_mate.c b/samtools/bam_mate.c
deleted file mode 100644
index 61f808a..0000000
--- a/samtools/bam_mate.c
+++ /dev/null
@@ -1,70 +0,0 @@
-#include <stdlib.h>
-#include <string.h>
-#include "bam.h"
-
-// currently, this function ONLY works if each read has one hit
-void bam_mating_core(bamFile in, bamFile out)
-{
-	bam_header_t *header;
-	bam1_t *b[2];
-	int curr, has_prev;
-
-	header = bam_header_read(in);
-	bam_header_write(out, header);
-
-	b[0] = bam_init1();
-	b[1] = bam_init1();
-	curr = 0; has_prev = 0;
-	while (bam_read1(in, b[curr]) >= 0) {
-		bam1_t *cur = b[curr], *pre = b[1-curr];
-		if (has_prev) {
-			if (strcmp(bam1_qname(cur), bam1_qname(pre)) == 0) { // identical pair name
-				cur->core.mtid = pre->core.tid; cur->core.mpos = pre->core.pos;
-				pre->core.mtid = cur->core.tid; pre->core.mpos = cur->core.pos;
-				if (pre->core.tid == cur->core.tid && !(cur->core.flag&(BAM_FUNMAP|BAM_FMUNMAP))
-					&& !(pre->core.flag&(BAM_FUNMAP|BAM_FMUNMAP)))
-				{
-					uint32_t cur5, pre5;
-					cur5 = (cur->core.flag&BAM_FREVERSE)? bam_calend(&cur->core, bam1_cigar(cur)) : cur->core.pos;
-					pre5 = (pre->core.flag&BAM_FREVERSE)? bam_calend(&pre->core, bam1_cigar(pre)) : pre->core.pos;
-					cur->core.isize = pre5 - cur5; pre->core.isize = cur5 - pre5;
-				} else cur->core.isize = pre->core.isize = 0;
-				if (pre->core.flag&BAM_FREVERSE) cur->core.flag |= BAM_FMREVERSE;
-				else cur->core.flag &= ~BAM_FMREVERSE;
-				if (cur->core.flag&BAM_FREVERSE) pre->core.flag |= BAM_FMREVERSE;
-				else pre->core.flag &= ~BAM_FMREVERSE;
-				if (cur->core.flag & BAM_FUNMAP) { pre->core.flag |= BAM_FMUNMAP; pre->core.flag &= ~BAM_FPROPER_PAIR; }
-				if (pre->core.flag & BAM_FUNMAP) { cur->core.flag |= BAM_FMUNMAP; cur->core.flag &= ~BAM_FPROPER_PAIR; }
-				bam_write1(out, pre);
-				bam_write1(out, cur);
-				has_prev = 0;
-			} else { // unpaired or singleton
-				pre->core.mtid = -1; pre->core.mpos = -1; pre->core.isize = 0;
-				if (pre->core.flag & BAM_FPAIRED) {
-					pre->core.flag |= BAM_FMUNMAP;
-					pre->core.flag &= ~BAM_FMREVERSE & ~BAM_FPROPER_PAIR;
-				}
-				bam_write1(out, pre);
-			}
-		} else has_prev = 1;
-		curr = 1 - curr;
-	}
-	if (has_prev) bam_write1(out, b[1-curr]);
-	bam_header_destroy(header);
-	bam_destroy1(b[0]);
-	bam_destroy1(b[1]);
-}
-
-int bam_mating(int argc, char *argv[])
-{
-	bamFile in, out;
-	if (argc < 3) {
-		fprintf(stderr, "samtools fixmate <in.nameSrt.bam> <out.nameSrt.bam>\n");
-		return 1;
-	}
-	in = (strcmp(argv[1], "-") == 0)? bam_dopen(fileno(stdin), "r") : bam_open(argv[1], "r");
-    out = (strcmp(argv[2], "-") == 0)? bam_dopen(fileno(stdout), "w") : bam_open(argv[2], "w");
-	bam_mating_core(in, out);
-	bam_close(in); bam_close(out);
-	return 0;
-}