From ca61fe3ad5a9d4b7d2acf2a780e637b28f056fce Mon Sep 17 00:00:00 2001
From: Heng Li <lh3@me.com>
Date: Mon, 8 Sep 2014 08:52:02 -0400
Subject: [PATCH] code backup

---
 bwamem.c | 22 +++++++++++++++-------
 bwamem.h |  2 +-
 2 files changed, 16 insertions(+), 8 deletions(-)

diff --git a/bwamem.c b/bwamem.c
index 0bbdd2b..d6a7998 100644
--- a/bwamem.c
+++ b/bwamem.c
@@ -377,7 +377,7 @@ KSORT_INIT(mem_ars2, mem_alnreg_t, alnreg_slt2)
 #define alnreg_slt(a, b) ((a).score > (b).score || ((a).score == (b).score && ((a).rb < (b).rb || ((a).rb == (b).rb && (a).qb < (b).qb))))
 KSORT_INIT(mem_ars, mem_alnreg_t, alnreg_slt)
 
-#define alnreg_hlt(a, b) ((a).score > (b).score || ((a).score == (b).score && (a).hash < (b).hash))
+#define alnreg_hlt(a, b) ((a).is_alt < (b).is_alt || ((a).is_alt == (b).is_alt && ((a).score > (b).score || ((a).score == (b).score && (a).hash < (b).hash))))
 KSORT_INIT(mem_ars_hash, mem_alnreg_t, alnreg_hlt)
 
 #define PATCH_MAX_R_BW 0.05f
@@ -475,14 +475,17 @@ int mem_test_and_remove_exact(const mem_opt_t *opt, int n, mem_alnreg_t *a, int
 	return n - 1;
 }
 
-void mem_mark_primary_se(const mem_opt_t *opt, int n, mem_alnreg_t *a, int64_t id)
+void mem_mark_primary_se(const mem_opt_t *opt, int _n, mem_alnreg_t *a, int64_t id)
 { // similar to the loop in mem_chain_flt()
-	int i, k, tmp;
+	int i, k, tmp, n;
 	kvec_t(int) z;
-	if (n == 0) return;
+	if (n_ == 0) return;
 	kv_init(z);
-	for (i = 0; i < n; ++i) a[i].sub = 0, a[i].secondary = -1, a[i].hash = hash_64(id+i);
-	ks_introsort(mem_ars_hash, n, a);
+	for (i = 0; i < n_; ++i) a[i].sub = 0, a[i].secondary = -1, a[i].hash = hash_64(id+i);
+	ks_introsort(mem_ars_hash, n_, a);
+	for (i = 0; i < n_; ++i)
+		if (a[i].is_alt) break;
+	if ((n = i) == 0) return;
 	tmp = opt->a + opt->b;
 	tmp = opt->o_del + opt->e_del > tmp? opt->o_del + opt->e_del : tmp;
 	tmp = opt->o_ins + opt->e_ins > tmp? opt->o_ins + opt->e_ins : tmp;
@@ -995,6 +998,11 @@ mem_alnreg_v mem_align1_core(const mem_opt_t *opt, const bwt_t *bwt, const bntse
 			printf("** %d, [%d,%d) <=> [%ld,%ld)\n", p->score, p->qb, p->qe, (long)p->rb, (long)p->re);
 		}
 	}
+	for (i = 0; i < regs.n; ++i) {
+		mem_alnreg_t *p = &regs.a[i];
+		if (p->rid >= 0 && bns->anns[p->rid].is_alt)
+			p->is_alt = 1;
+	}
 	return regs;
 }
 
@@ -1077,7 +1085,7 @@ typedef struct {
 	const mem_pestat_t *pes;
 	smem_aux_t **aux;
 	bseq1_t *seqs;
-	mem_alnreg_v *regs, *regs_alt;
+	mem_alnreg_v *regs;
 	int64_t n_processed;
 } worker_t;
 
diff --git a/bwamem.h b/bwamem.h
index 61bb335..8b8ec0d 100644
--- a/bwamem.h
+++ b/bwamem.h
@@ -68,7 +68,7 @@ typedef struct {
 	int seedcov;    // length of regions coverged by seeds
 	int secondary;  // index of the parent hit shadowing the current hit; <0 if primary
 	int seedlen0;   // length of the starting seed
-	int n_comp;     // number of sub-alignments chained together
+	int n_comp:30, is_alt:2; // number of sub-alignments chained together
 	float frac_rep;
 	uint64_t hash;
 } mem_alnreg_t;