lh3 · BenLangmead · Oct 17, 2017
diff --git a/bwamem.c b/bwamem.c
@@ -505,6 +505,8 @@ static void mem_mark_primary_se_core(const mem_opt_t *opt, int n, mem_alnreg_t *
 			int e_min = a[j].qe < a[i].qe? a[j].qe : a[i].qe;
 			if (e_min > b_max) { // have overlap
 				int min_l = a[i].qe - a[i].qb < a[j].qe - a[j].qb? a[i].qe - a[i].qb : a[j].qe - a[j].qb;
+				a[j].osub = a[j].osub < a[i].score ? a[i].score : a[j].osub;
+				a[j].osub_n++;
 				if (e_min - b_max >= min_l * opt->mask_level) { // significant overlap
 					if (a[j].sub == 0) a[j].sub = a[i].score;
 					if (a[j].score - a[i].score <= tmp && (a[j].is_alt || !a[i].is_alt))
@@ -942,6 +944,52 @@ void mem_aln2sam(const mem_opt_t *opt, const bntseq_t *bns, kstring_t *str, bseq
 		for (i = tmp; i < str->l; ++i) // replace TAB in the comment to SPACE
 			if (str->s[i] == '\t') str->s[i] = ' ';
 	}
+	if ((p->flag & 4) == 0) {
+		kputsn("\tZT:Z:", 6, str);
+		kputw(p->score, str); // same as AS:i, ztz0
+		kputc(',', str);
+		if(p->n_cigar) {
+			kputw(p->NM, str); // ztz1
+		} else {
+			kputsn("NA", 2, str);
+		}
+		kputc(',', str);
+		if(p->sub >= 0) {
+			kputw(p->score - p->sub, str); // ztz2
+		} else {
+			kputsn("NA", 2, str);
+		}
+		kputc(',', str);
+		if(p->osub >= 0) {
+			kputw(p->score - p->osub, str); // ztz3
+		} else {
+			kputsn("NA", 2, str);
+		}
+		kputc(',', str);
+		kputw(p->pair_score, str); // ztz4
+		kputc(',', str);
+		if(p->pair_sub >= 0) {
+			kputw(p->pair_score - p->pair_sub, str); // ztz5
+		} else {
+			kputsn("NA", 2, str);
+		}
+		kputc(',', str);
+		kputw(p->seedlen0, str); // ztz6
+		kputc(',', str);
+		kputw(p->sub_n, str); // ztz7
+		kputc(',', str);
+		kputw(p->osub_n, str); // ztz8
+		kputc(',', str);
+		kputw(p->pair_nsub, str); // ztz9
+		kputc(',', str);
+		kputw((int)(p->frac_rep * 1000.0), str); // ztz10
+		kputc(',', str);
+		kputw((int)(p->pair_frac_rep * 1000.0), str); // ztz11
+		kputc(',', str);
+		kputw((int)(p->seedcov * 1000.0), str); // ztz12
+		kputc(',', str);
+		kputw((int)(p->pair_seedcov * 1000.0), str); // ztz13
+	}
 	kputc('\n', str);
 }
 
@@ -1152,8 +1200,17 @@ mem_aln_t mem_reg2aln(const mem_opt_t *opt, const bntseq_t *bns, const uint8_t *
 	a.rid = bns_pos2rid(bns, pos);
 	assert(a.rid == ar->rid);
 	a.pos = pos - bns->anns[a.rid].offset;
-	a.score = ar->score; a.sub = ar->sub > ar->csub? ar->sub : ar->csub;
+	a.score = ar->score;
+	a.sub = ar->sub > ar->csub? ar->sub : ar->csub;
+	a.osub = ar->osub;
 	a.is_alt = ar->is_alt; a.alt_sc = ar->alt_sc;
+	a.seedlen0 = ar->seedlen0;
+	a.n_comp = ar->n_comp;
+	a.seedcov = ((float)ar->seedcov) / l_query;
+	a.frac_rep = ar->frac_rep;
+	a.sub_n = ar->sub_n; a.osub_n = ar->osub_n;
+	a.pair_score = a.pair_sub = a.pair_nsub = 0;
+	a.pair_frac_rep = a.pair_seedcov = 0.;
 	free(query);
 	return a;
 }

diff --git a/bwamem.h b/bwamem.h
@@ -63,9 +63,11 @@ typedef struct {
 	int score;      // best local SW score
 	int truesc;     // actual score corresponding to the aligned region; possibly smaller than $score
 	int sub;        // 2nd best SW score
+	int osub;       // more liberal 2nd best SW score
 	int alt_sc;
 	int csub;       // SW score of a tandem hit
 	int sub_n;      // approximate number of suboptimal hits
+	int osub_n;     // more liberal approximate number of suboptimal hits
 	int w;          // actual band width used in extension
 	int seedcov;    // length of regions coverged by seeds
 	int secondary;  // index of the parent hit shadowing the current hit; <0 if primary
@@ -93,7 +95,11 @@ typedef struct { // This struct is only used for the convenience of API.
 	uint32_t *cigar; // CIGAR in the BAM encoding: opLen<<4|op; op to integer mapping: MIDSH=>01234
 	char *XA;        // alternative mappings
 
-	int score, sub, alt_sc;
+	int score, sub, osub, alt_sc;
+	float seedcov, pair_seedcov;
+	int sub_n, osub_n, pair_score, pair_sub, pair_nsub;
+	float frac_rep, pair_frac_rep;
+	int seedlen0, n_comp;
 } mem_aln_t;
 
 #ifdef __cplusplus

diff --git a/bwamem_pair.c b/bwamem_pair.c
@@ -351,6 +351,21 @@ int mem_sam_pe(const mem_opt_t *opt, const bntseq_t *bns, const uint8_t *pac, co
 				aa[i][n_aa[i]++] = g[i];
 			}
 		}
+		// Might be less work if we installed these earlier
+		h[0].pair_score = h[1].pair_score = o;
+		h[0].pair_sub = h[1].pair_sub = subo;
+		h[0].pair_nsub = h[1].pair_nsub = n_sub;
+		h[0].pair_frac_rep = h[1].pair_frac_rep = a[0].a[0].frac_rep + a[1].a[0].frac_rep;
+		h[0].pair_seedcov = h[1].pair_seedcov = ((float)(a[0].a[0].seedcov + a[1].a[0].seedcov)) / (s[0].l_seq + s[1].l_seq);
+		for (j = 0; j < 2; ++j) {
+			for (i = 0; i < n_aa[j]; ++i) {
+				aa[j][i].pair_score = h[j].pair_score;
+				aa[j][i].pair_sub = h[j].pair_sub;
+				aa[j][i].pair_nsub = h[j].pair_nsub;
+				aa[j][i].pair_frac_rep = h[j].pair_frac_rep;
+				aa[j][i].pair_seedcov = h[j].pair_seedcov;
+			}
+		}
 		for (i = 0; i < n_aa[0]; ++i)
 			mem_aln2sam(opt, bns, &str, &s[0], n_aa[0], aa[0], i, &h[1]); // write read1 hits
 		s[0].sam = strdup(str.s); str.l = 0;