Merge branch 'dev'

bwamem.c

@@ -78,6 +78,7 @@ mem_opt_t *mem_opt_init()
 	o->min_chain_weight = 0;
 	o->max_chain_extend = 1<<30;
 	o->mapQ_coef_len = 50; o->mapQ_coef_fac = log(o->mapQ_coef_len);
+	o->min_pa_ratio = 0.8;
 	bwa_fill_scmat(o->a, o->b, o->mat);
 	return o;
 }
@@ -514,14 +515,18 @@ int mem_mark_primary_se(const mem_opt_t *opt, int n, mem_alnreg_t *a, int64_t id
 	int_v z = {0,0,0};
 	if (n == 0) return 0;
 	for (i = n_pri = 0; i < n; ++i) {
-		a[i].sub = 0, a[i].secondary = -1, a[i].hash = hash_64(id+i);
+		a[i].sub = 0, a[i].alt_sc = 0, a[i].secondary = -1, a[i].hash = hash_64(id+i);
 		if (!a[i].is_alt) ++n_pri;
 	}
 	ks_introsort(mem_ars_hash, n, a);
 	mem_mark_primary_se_core(opt, n, a, &z);
-	for (i = 0; i < n; ++i) // don't track the "parent" hit of ALT secondary hits
-		if (a[i].is_alt && a[i].secondary >= 0)
-			a[i].secondary = INT_MAX;
+	for (i = 0; i < n; ++i) {
+		mem_alnreg_t *p = &a[i];
+		if (p->is_alt && p->secondary >= 0) // don't track the "parent" hit of ALT secondary hits
+			p->secondary = INT_MAX;
+		if (!p->is_alt && p->secondary >= 0 && a[p->secondary].is_alt)
+			p->alt_sc = a[p->secondary].score;
+	}
 	if (n_pri > 0 || n_pri != n) {
 		ks_introsort(mem_ars_hash2, n, a);
 		for (i = 0; i < n_pri; ++i) a[i].sub = 0, a[i].secondary = -1;
@@ -808,7 +813,7 @@ void mem_aln2sam(const mem_opt_t *opt, const bntseq_t *bns, kstring_t *str, bseq
 	if (p->rid >= 0) { // with coordinate
 		kputs(bns->anns[p->rid].name, str); kputc('\t', str); // RNAME
 		kputl(p->pos + 1, str); kputc('\t', str); // POS
-		kputw(p->mapq, str); kputc('\t', str); // MAPQ
+		kputw(p->score < opt->min_pa_ratio * p->alt_sc? 0 : p->mapq, str); kputc('\t', str); // MAPQ
 		if (p->n_cigar) { // aligned
 			for (i = 0; i < p->n_cigar; ++i) {
 				int c = p->cigar[i]&0xf;
@@ -880,13 +885,11 @@ void mem_aln2sam(const mem_opt_t *opt, const bntseq_t *bns, kstring_t *str, bseq
 		for (i = 0; i < n; ++i)
 			if (i != which && !(list[i].flag&0x100)) break;
 		if (i < n) { // there are other primary hits; output them
-			int pri_alt_sc = -1;
 			kputsn("\tSA:Z:", 6, str);
 			for (i = 0; i < n; ++i) {
 				const mem_aln_t *r = &list[i];
 				int k;
-				if (i == which || (list[i].flag&0x100)) continue; // proceed if: 1) different from the current; 2) not shadowed multi hit
-				if (list[i].is_alt) pri_alt_sc = pri_alt_sc > r->score? pri_alt_sc : r->score;
+				if (i == which || (r->flag&0x100)) continue; // proceed if: 1) different from the current; 2) not shadowed multi hit
 				kputs(bns->anns[r->rid].name, str); kputc(',', str);
 				kputl(r->pos+1, str); kputc(',', str);
 				kputc("+-"[r->is_rev], str); kputc(',', str);
@@ -897,9 +900,11 @@ void mem_aln2sam(const mem_opt_t *opt, const bntseq_t *bns, kstring_t *str, bseq
 				kputc(',', str); kputw(r->NM, str);
 				kputc(';', str);
 			}
-			if (pri_alt_sc > 0)
-				ksprintf(str, "\tpa:f:%.3f", (double)p->score / pri_alt_sc);
 		}
+		if (p->alt_sc > 0)
+			ksprintf(str, "\tpa:f:%.3f", (double)p->score / p->alt_sc);
+		if (p->score < opt->min_pa_ratio * p->alt_sc)
+			ksprintf(str, "\tom:i:%d", p->mapq);
 	}
 	if (p->XA) { kputsn("\tXA:Z:", 6, str); kputs(p->XA, str); }
 	if (s->comment) { kputc('\t', str); kputs(s->comment, str); }
@@ -1098,7 +1103,7 @@ mem_aln_t mem_reg2aln(const mem_opt_t *opt, const bntseq_t *bns, const uint8_t *
 	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.is_alt = ar->is_alt;
+	a.is_alt = ar->is_alt; a.alt_sc = ar->alt_sc;
 	free(query);
 	return a;
 }

bwamem.h

@@ -48,6 +48,7 @@ typedef struct {
 	float XA_drop_ratio;    // when counting hits for the XA tag, ignore alignments with score < XA_drop_ratio * max_score; only effective for the XA tag
 	float mask_level_redun;
 	float mapQ_coef_len;
+	float min_pa_ratio;
 	int mapQ_coef_fac;
 	int max_ins;            // when estimating insert size distribution, skip pairs with insert longer than this value
 	int max_matesw;         // perform maximally max_matesw rounds of mate-SW for each end
@@ -62,6 +63,7 @@ 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 alt_sc;
 	int csub;       // SW score of a tandem hit
 	int sub_n;      // approximate number of suboptimal hits
 	int w;          // actual band width used in extension
@@ -90,7 +92,7 @@ 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;
+	int score, sub, alt_sc;
 } mem_aln_t;
 
 #ifdef __cplusplus

bwamem_pair.c

@@ -240,14 +240,26 @@ int mem_pair(const mem_opt_t *opt, const bntseq_t *bns, const uint8_t *pac, cons
 	return ret;
 }
 
+void mem_aln2sam(const mem_opt_t *opt, const bntseq_t *bns, kstring_t *str, bseq1_t *s, int n, const mem_aln_t *list, int which, const mem_aln_t *m);
+
+static inline void mem_reg2sam_alt(const mem_opt_t *opt, const bntseq_t *bns, const uint8_t *pac, kstring_t *str, bseq1_t *s, mem_alnreg_t *p, int extra_flag, const mem_aln_t *m)
+{ // a simplified version of mem_reg2sam()
+	mem_aln_t t;
+	if (p->score < opt->T || p->secondary >= 0 || !p->is_alt) return;
+	t = mem_reg2aln(opt, bns, pac, s->l_seq, s->seq, p);
+	t.flag |= extra_flag;
+	t.flag |= (opt->flag&MEM_F_NO_MULTI)? 0x10000 : 0x800;
+	mem_aln2sam(opt, bns, str, s, 1, &t, 0, m);
+	free(t.cigar);
+}
+
 #define raw_mapq(diff, a) ((int)(6.02 * (diff) / (a) + .499))
 
 int mem_sam_pe(const mem_opt_t *opt, const bntseq_t *bns, const uint8_t *pac, const mem_pestat_t pes[4], uint64_t id, bseq1_t s[2], mem_alnreg_v a[2])
 {
 	extern int mem_mark_primary_se(const mem_opt_t *opt, int n, mem_alnreg_t *a, int64_t id);
 	extern int mem_approx_mapq_se(const mem_opt_t *opt, const mem_alnreg_t *a);
 	extern void mem_reg2sam(const mem_opt_t *opt, const bntseq_t *bns, const uint8_t *pac, bseq1_t *s, mem_alnreg_v *a, int extra_flag, const mem_aln_t *m);
-	extern void mem_aln2sam(const mem_opt_t *opt, const bntseq_t *bns, kstring_t *str, bseq1_t *s, int n, const mem_aln_t *list, int which, const mem_aln_t *m);
 	extern char **mem_gen_alt(const mem_opt_t *opt, const bntseq_t *bns, const uint8_t *pac, const mem_alnreg_v *a, int l_query, const char *query);
 
 	int n = 0, i, j, z[2], o, subo, n_sub, extra_flag = 1, n_pri[2];
@@ -327,8 +339,12 @@ int mem_sam_pe(const mem_opt_t *opt, const bntseq_t *bns, const uint8_t *pac, co
 		// write SAM
 		h[0] = mem_reg2aln(opt, bns, pac, s[0].l_seq, s[0].seq, &a[0].a[z[0]]); h[0].mapq = q_se[0]; h[0].flag |= 0x40 | extra_flag; h[0].XA = XA[0]? XA[0][z[0]] : 0;
 		h[1] = mem_reg2aln(opt, bns, pac, s[1].l_seq, s[1].seq, &a[1].a[z[1]]); h[1].mapq = q_se[1]; h[1].flag |= 0x80 | extra_flag; h[1].XA = XA[1]? XA[1][z[1]] : 0;
-		mem_aln2sam(opt, bns, &str, &s[0], 1, &h[0], 0, &h[1]); s[0].sam = strdup(str.s); str.l = 0;
-		mem_aln2sam(opt, bns, &str, &s[1], 1, &h[1], 0, &h[0]); s[1].sam = str.s;
+		mem_aln2sam(opt, bns, &str, &s[0], 1, &h[0], 0, &h[1]); // write the primary hit for read1
+		if (n_pri[0] < a[0].n) mem_reg2sam_alt(opt, bns, pac, &str, &s[0], &a[0].a[n_pri[0]], 0x41|extra_flag, &h[1]);
+		s[0].sam = strdup(str.s); str.l = 0;
+		mem_aln2sam(opt, bns, &str, &s[1], 1, &h[1], 0, &h[0]); // write the primary hit for read2
+		if (n_pri[1] < a[1].n) mem_reg2sam_alt(opt, bns, pac, &str, &s[1], &a[1].a[n_pri[1]], 0x81|extra_flag, &h[0]);
+		s[1].sam = str.s;
 		if (strcmp(s[0].name, s[1].name) != 0) err_fatal(__func__, "paired reads have different names: \"%s\", \"%s\"\n", s[0].name, s[1].name);
 		free(h[0].cigar); // h[0].XA will be freed in the following block
 		free(h[1].cigar);

fastmap.c

@@ -55,7 +55,7 @@ int main_mem(int argc, char *argv[])
 
 	opt = mem_opt_init();
 	memset(&opt0, 0, sizeof(mem_opt_t));
-	while ((c = getopt(argc, argv, "epaFMCSPHVYk:c:v:s:r:t:R:A:B:O:E:U:w:L:d:T:Q:D:m:I:N:W:x:G:h:y:K:")) >= 0) {
+	while ((c = getopt(argc, argv, "epaFMCSPHVYk:c:v:s:r:t:R:A:B:O:E:U:w:L:d:T:Q:D:m:I:N:W:x:G:h:y:K:g:")) >= 0) {
 		if (c == 'k') opt->min_seed_len = atoi(optarg), opt0.min_seed_len = 1;
 		else if (c == 'x') mode = optarg;
 		else if (c == 'w') opt->w = atoi(optarg), opt0.w = 1;
@@ -85,6 +85,7 @@ int main_mem(int argc, char *argv[])
 		else if (c == 'N') opt->max_chain_extend = atoi(optarg), opt0.max_chain_extend = 1;
 		else if (c == 'W') opt->min_chain_weight = atoi(optarg), opt0.min_chain_weight = 1;
 		else if (c == 'y') opt->max_mem_intv = atol(optarg), opt0.max_mem_intv = 1;
+		else if (c == 'g') opt->min_pa_ratio = atof(optarg), opt0.min_pa_ratio = 1;
 		else if (c == 'C') copy_comment = 1;
 		else if (c == 'K') fixed_chunk_size = atoi(optarg);
 		else if (c == 'Q') {
@@ -138,7 +139,7 @@ int main_mem(int argc, char *argv[])
 		fprintf(stderr, "       -w INT        band width for banded alignment [%d]\n", opt->w);
 		fprintf(stderr, "       -d INT        off-diagonal X-dropoff [%d]\n", opt->zdrop);
 		fprintf(stderr, "       -r FLOAT      look for internal seeds inside a seed longer than {-k} * FLOAT [%g]\n", opt->split_factor);
-		fprintf(stderr, "       -y INT        find MEMs longer than {-k} * {-r} with size less than INT [%ld]\n", (long)opt->max_mem_intv);
+		fprintf(stderr, "       -y INT        find MEMs longer than {-k} * {-r} with size less than INT (EXPERIMENTAL) [%ld]\n", (long)opt->max_mem_intv);
 //		fprintf(stderr, "       -s INT        look for internal seeds inside a seed with less than INT occ [%d]\n", opt->split_width);
 		fprintf(stderr, "       -c INT        skip seeds with more than INT occurrences [%d]\n", opt->max_occ);
 		fprintf(stderr, "       -D FLOAT      drop chains shorter than FLOAT fraction of the longest overlapping chain [%.2f]\n", opt->drop_ratio);
@@ -164,6 +165,7 @@ int main_mem(int argc, char *argv[])
 		fprintf(stderr, "       -R STR        read group header line such as '@RG\\tID:foo\\tSM:bar' [null]\n");
 		fprintf(stderr, "\n");
 		fprintf(stderr, "       -v INT        verbose level: 1=error, 2=warning, 3=message, 4+=debugging [%d]\n", bwa_verbose);
+		fprintf(stderr, "       -g FLOAT      set mapQ to zero if the ratio of the primary-to-alt scores below FLOAT [%.3f]\n", opt->min_pa_ratio);
 		fprintf(stderr, "       -T INT        minimum score to output [%d]\n", opt->T);
 		fprintf(stderr, "       -h INT        if there are <INT hits with score >80%% of the max score, output all in XA [%d]\n", opt->max_hits);
 		fprintf(stderr, "       -a            output all alignments for SE or unpaired PE\n");

main.c

@@ -4,7 +4,7 @@
 #include "utils.h"
 
 #ifndef PACKAGE_VERSION
-#define PACKAGE_VERSION "0.7.10-r849-dirty"
+#define PACKAGE_VERSION "0.7.10-r855-dirty"
 #endif
 
 int bwa_fa2pac(int argc, char *argv[]);