X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=misc%2Fmaq2sam.c;h=2bfbe2a3b328e276b52f1a443dbc6500d81122e8;hb=307c147168f7154e3755712797078c513e0b242a;hp=e30aa925784198aab70132184a2dddb6f2e7705d;hpb=f93dae0d03856955f9424e8b2aaf261304ca647e;p=samtools.git

diff --git a/misc/maq2sam.c b/misc/maq2sam.c
index e30aa92..2bfbe2a 100644
--- a/misc/maq2sam.c
+++ b/misc/maq2sam.c
@@ -5,6 +5,8 @@
 #include <stdlib.h>
 #include <assert.h>
 
+#define PACKAGE_VERSION "r439"
+
 //#define MAQ_LONGREADS
 
 #ifdef MAQ_LONGREADS
@@ -84,7 +86,7 @@ maqmap_t *maqmap_read_header(gzFile fp)
 	return mm;
 }
 
-void maq2tam_core(gzFile fp)
+void maq2tam_core(gzFile fp, const char *rg)
 {
 	maqmap_t *mm;
 	maqmap1_t mm1, *m1;
@@ -92,7 +94,7 @@ void maq2tam_core(gzFile fp)
 	m1 = &mm1;
 	mm = maqmap_read_header(fp);
 	while ((ret = gzread(fp, m1, sizeof(maqmap1_t))) == sizeof(maqmap1_t)) {
-		int j, flag = 0;
+		int j, flag = 0, se_mapq = m1->seq[MAX_READLEN-1];
 		if (m1->flag) flag |= 1;
 		if ((m1->flag&PAIRFLAG_PAIRED) || ((m1->flag&PAIRFLAG_SW) && m1->flag != 192)) flag |= 2;
 		if (m1->flag == 192) flag |= 4;
@@ -109,9 +111,9 @@ void maq2tam_core(gzFile fp)
 				else if (m1->flag&(PAIRFLAG_RF|PAIRFLAG_RR)) c = 1;
 				else c = m1->pos&1;
 			}
-			flag |= c;
+			if (c) flag |= 0x20;
 		}
-		if (flag) {
+		if (m1->flag) {
 			int l = strlen(m1->name);
 			if (m1->name[l-2] == '/') {
 				flag |= (m1->name[l-1] == '1')? 0x40 : 0x80;
@@ -128,6 +130,7 @@ void maq2tam_core(gzFile fp)
 				if (c > 0) printf("%dM%dI%dM\t", m1->map_qual, c, m1->size - m1->map_qual - c);
 				else printf("%dM%dD%dM\t", m1->map_qual, -c, m1->size - m1->map_qual);
 			}
+			se_mapq = 0; // zero SE mapQ for reads aligned by SW
 		} else {
 			if (flag&4) printf("0\t*\t");
 			else printf("%d\t%dM\t", m1->map_qual, m1->size);
@@ -141,11 +144,12 @@ void maq2tam_core(gzFile fp)
 		for (j = 0; j != m1->size; ++j)
 			putchar((m1->seq[j]&0x3f) + 33);
 		putchar('\t');
-		if (flag&4) {
+		if (rg) printf("RG:Z:%s\t", rg);
+		if (flag&4) { // unmapped
 			printf("MF:i:%d\n", m1->flag);
 		} else {
 			printf("MF:i:%d\t", m1->flag);
-			if (m1->flag) printf("Aq:i:%d\t", m1->alt_qual);
+			if (m1->flag) printf("AM:i:%d\tSM:i:%d\t", m1->alt_qual, se_mapq);
 			printf("NM:i:%d\tUQ:i:%d\tH0:i:%d\tH1:i:%d\n", m1->info1&0xf, m1->info2, m1->c[0], m1->c[1]);
 		}
 	}
@@ -158,11 +162,12 @@ int main(int argc, char *argv[])
 {
 	gzFile fp;
 	if (argc == 1) {
-		fprintf(stderr, "Usage: maq2tam <in.map>\n");
+		fprintf(stderr, "Version: %s\n", PACKAGE_VERSION);
+		fprintf(stderr, "Usage: maq2sam <in.map> [<readGroup>]\n");
 		return 1;
 	}
 	fp = strcmp(argv[1], "-")? gzopen(argv[1], "r") : gzdopen(fileno(stdin), "r");
-	maq2tam_core(fp);
+	maq2tam_core(fp, argc > 2? argv[2] : 0);
 	gzclose(fp);
 	return 0;
 }