From 7cc613bfb6f35f6ef81e79ab91efdb703573dad7 Mon Sep 17 00:00:00 2001
From: Noah Kessler <njk40@cam.ac.uk>
Date: Fri, 8 Jan 2021 01:08:33 +0000
Subject: [PATCH] Fix CIGAR parsing bug

Previously, only the last operation of the CIGAR string was recorded in record->cigar.
This caused basecalls to be ignored and/or placed at the wrong reference position.
This has now been corrected and the CIGAR string is recorded properly.
---
 sam_funcs.c | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/sam_funcs.c b/sam_funcs.c
index 7d89897..7685f88 100644
--- a/sam_funcs.c
+++ b/sam_funcs.c
@@ -184,8 +184,9 @@ int parseBuffer(bam_header_t *header, bam1_t *b, MapRecord* record, unsigned int
     if(c->qual < mapqThr)
         return 1;
     // 6 - CIGAR
+	record->cigar[0] = '\0';
     for (i = 0; i < c->n_cigar; ++i)
-        sprintf(record->cigar, "%d%c", bam1_cigar(b)[i]>>BAM_CIGAR_SHIFT, "MIDNSHP"[bam1_cigar(b)[i]&BAM_CIGAR_MASK]);
+        sprintf(record->cigar, "%s%d%c", record->cigar, bam1_cigar(b)[i]>>BAM_CIGAR_SHIFT, "MIDNSHP"[bam1_cigar(b)[i]&BAM_CIGAR_MASK]);
     // 10 - SEQ
     for(i = 0; i < c->l_qseq; ++i)
         record->seqBuf[i] = bam_nt16_rev_table[bam1_seqi(s, i)];