X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=bam_mate.c;h=642ded68b80c0da699ba0091dc7e5dd9acc36d96;hb=df50415f5380510f5b44bee2361413fc39c8bbcf;hp=61f808a26402e9bd1d332f40074b4b3ca1f89dd3;hpb=4efe4317c377019fbb64bcfae519403a3a9d1f5f;p=samtools.git

diff --git a/bam_mate.c b/bam_mate.c
index 61f808a..642ded6 100644
--- a/bam_mate.c
+++ b/bam_mate.c
@@ -1,14 +1,43 @@
 #include <stdlib.h>
 #include <string.h>
+#include "kstring.h"
 #include "bam.h"
 
+void bam_template_cigar(bam1_t *b1, bam1_t *b2, kstring_t *str)
+{
+	bam1_t *swap;
+	int i, end;
+	uint32_t *cigar;
+	str->l = 0;
+	if (b1->core.tid != b2->core.tid || b1->core.tid < 0) return; // coordinateless or not on the same chr; skip
+	if (b1->core.pos > b2->core.pos) swap = b1, b1 = b2, b2 = swap; // make sure b1 has a smaller coordinate
+	kputc((b1->core.flag & BAM_FREAD1)? '1' : '2', str); // segment index
+	kputc((b1->core.flag & BAM_FREVERSE)? 'R' : 'F', str); // strand
+	for (i = 0, cigar = bam1_cigar(b1); i < b1->core.n_cigar; ++i) {
+		kputw(bam_cigar_oplen(cigar[i]), str);
+		kputc(bam_cigar_opchr(cigar[i]), str);
+	}
+	end = bam_calend(&b1->core, cigar);
+	kputw(b2->core.pos - end, str);
+	kputc('T', str);
+	kputc((b2->core.flag & BAM_FREAD1)? '1' : '2', str); // segment index
+	kputc((b2->core.flag & BAM_FREVERSE)? 'R' : 'F', str); // strand
+	for (i = 0, cigar = bam1_cigar(b2); i < b2->core.n_cigar; ++i) {
+		kputw(bam_cigar_oplen(cigar[i]), str);
+		kputc(bam_cigar_opchr(cigar[i]), str);
+	}
+	bam_aux_append(b1, "CT", 'Z', str->l+1, (uint8_t*)str->s); 
+}
+
 // 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;
+	int curr, has_prev, pre_end, cur_end;
+	kstring_t str;
 
+	str.l = str.m = 0; str.s = 0;
 	header = bam_header_read(in);
 	bam_header_write(out, header);
 
@@ -17,16 +46,20 @@ void bam_mating_core(bamFile in, bamFile out)
 	curr = 0; has_prev = 0;
 	while (bam_read1(in, b[curr]) >= 0) {
 		bam1_t *cur = b[curr], *pre = b[1-curr];
+		if (cur->core.tid < 0) continue;
+		cur_end = bam_calend(&cur->core, bam1_cigar(cur));
+		if (cur_end > (int)header->target_len[cur->core.tid]) cur->core.flag |= BAM_FUNMAP;
+		if (cur->core.flag & BAM_FSECONDARY) continue; // skip secondary alignments
 		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)))
+					&& !(pre->core.flag&(BAM_FUNMAP|BAM_FMUNMAP))) // set TLEN/ISIZE
 				{
 					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;
+					cur5 = (cur->core.flag&BAM_FREVERSE)? cur_end : cur->core.pos;
+					pre5 = (pre->core.flag&BAM_FREVERSE)? pre_end : 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;
@@ -35,6 +68,7 @@ void bam_mating_core(bamFile in, bamFile out)
 				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_template_cigar(pre, cur, &str);
 				bam_write1(out, pre);
 				bam_write1(out, cur);
 				has_prev = 0;
@@ -48,18 +82,20 @@ void bam_mating_core(bamFile in, bamFile out)
 			}
 		} else has_prev = 1;
 		curr = 1 - curr;
+		pre_end = cur_end;
 	}
 	if (has_prev) bam_write1(out, b[1-curr]);
 	bam_header_destroy(header);
 	bam_destroy1(b[0]);
 	bam_destroy1(b[1]);
+	free(str.s);
 }
 
 int bam_mating(int argc, char *argv[])
 {
 	bamFile in, out;
 	if (argc < 3) {
-		fprintf(stderr, "samtools fixmate <in.nameSrt.bam> <out.nameSrt.bam>\n");
+		fprintf(stderr, "Usage: 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");