From 4b8b4418df99bde6649a7bf1b63efb32bc10fd61 Mon Sep 17 00:00:00 2001
From: Heng Li <lh3@me.com>
Date: Sun, 30 Mar 2025 19:30:19 -0400
Subject: [PATCH] r1236: support paired-end short-read RNA-seq

---
 map.c     | 14 +++++++++++++-
 minimap.h |  3 ++-
 options.c |  4 +++-
 3 files changed, 18 insertions(+), 3 deletions(-)

diff --git a/map.c b/map.c
index 038888f..8e10445 100644
--- a/map.c
+++ b/map.c
@@ -224,7 +224,7 @@ static mm_reg1_t *align_regs(const mm_mapopt_t *opt, const mm_idx_t *mi, void *k
 	return regs;
 }
 
-void mm_map_frag(const mm_idx_t *mi, int n_segs, const int *qlens, const char **seqs, int *n_regs, mm_reg1_t **regs, mm_tbuf_t *b, const mm_mapopt_t *opt, const char *qname)
+void mm_map_frag_core(const mm_idx_t *mi, int n_segs, const int *qlens, const char **seqs, int *n_regs, mm_reg1_t **regs, mm_tbuf_t *b, const mm_mapopt_t *opt, const char *qname)
 {
 	int i, j, rep_len, qlen_sum, n_regs0, n_mini_pos;
 	int max_chain_gap_qry, max_chain_gap_ref, is_splice = !!(opt->flag & MM_F_SPLICE), is_sr = !!(opt->flag & MM_F_SR);
@@ -373,6 +373,18 @@ void mm_map_frag(const mm_idx_t *mi, int n_segs, const int *qlens, const char **
 	}
 }
 
+void mm_map_frag(const mm_idx_t *mi, int n_segs, const int *qlens, const char **seqs, int *n_regs, mm_reg1_t **regs, mm_tbuf_t *b, const mm_mapopt_t *opt, const char *qname)
+{
+	if ((opt->flag & MM_F_PE_IND) && n_segs == 2 && opt->pe_ori >= 0 && (opt->flag&MM_F_CIGAR)) {
+		int i;
+		for (i = 0; i < n_segs; ++i)
+			mm_map_frag_core(mi, 1, &qlens[i], &seqs[i], &n_regs[i], &regs[i], b, opt, qname);
+		mm_pair(b->km, opt->max_gap_ref, opt->pe_bonus, opt->a * 2 + opt->b, opt->a, qlens, n_regs, regs);
+	} else {
+		mm_map_frag_core(mi, n_segs, qlens, seqs, n_regs, regs, b, opt, qname);
+	}
+}
+
 mm_reg1_t *mm_map(const mm_idx_t *mi, int qlen, const char *seq, int *n_regs, mm_tbuf_t *b, const mm_mapopt_t *opt, const char *qname)
 {
 	mm_reg1_t *regs;
diff --git a/minimap.h b/minimap.h
index 64dfe33..5efa6d0 100644
--- a/minimap.h
+++ b/minimap.h
@@ -5,7 +5,7 @@
 #include <stdio.h>
 #include <sys/types.h>
 
-#define MM_VERSION "2.28-r1235-dirty"
+#define MM_VERSION "2.28-r1236-dirty"
 
 #define MM_F_NO_DIAG       (0x001LL) // no exact diagonal hit
 #define MM_F_NO_DUAL       (0x002LL) // skip pairs where query name is lexicographically larger than target name
@@ -45,6 +45,7 @@
 #define MM_F_SPLICE_OLD    (0x800000000LL)
 #define MM_F_SECONDARY_SEQ (0x1000000000LL)	//output SEQ field for seqondary alignments using hard clipping
 #define MM_F_OUT_DS        (0x2000000000LL)
+#define MM_F_PE_IND        (0x4000000000LL)
 
 #define MM_I_HPC          0x1
 #define MM_I_NO_SEQ       0x2
diff --git a/options.c b/options.c
index d466682..ae11442 100644
--- a/options.c
+++ b/options.c
@@ -177,10 +177,12 @@ int mm_set_opt(const char *preset, mm_idxopt_t *io, mm_mapopt_t *mo)
 		if (strcmp(preset, "splice:hq") == 0) {
 			mo->noncan = 5, mo->b = 4, mo->q = 6, mo->q2 = 24;
 		} else if (strcmp(preset, "splice:sr") == 0) {
-			mo->flag |= MM_F_NO_PRINT_2ND | MM_F_2_IO_THREADS | MM_F_HEAP_SORT;
+			mo->flag |= MM_F_NO_PRINT_2ND | MM_F_2_IO_THREADS | MM_F_HEAP_SORT | MM_F_FRAG_MODE | MM_F_PE_IND;
 			mo->noncan = 5, mo->b = 4, mo->q = 6, mo->q2 = 24;
 			mo->end_bonus = 10;
 			mo->mini_batch_size = 50000000;
+			mo->pe_ori = 0<<1|1; // FR
+			mo->best_n = 10;
 		}
 	} else return -1;
 	return 0;