From e285a89362937c8b62428c2f4ff1a1beb5ad2c47 Mon Sep 17 00:00:00 2001
From: John Lees <lees.john6@gmail.com>
Date: Thu, 12 Oct 2023 14:52:17 +0100
Subject: [PATCH] Fix for multi-contig references in map

Short contigs may be skipped entirely due to no matches, so need to keep advancing writer
---
 src/ska_ref/aln_writer.rs | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/ska_ref/aln_writer.rs b/src/ska_ref/aln_writer.rs
index 7227fb4..1a8afb2 100644
--- a/src/ska_ref/aln_writer.rs
+++ b/src/ska_ref/aln_writer.rs
@@ -122,7 +122,7 @@ impl<'a> AlnWriter<'a> {
     /// Call in a loop over mapped positions, usually excluding '-' base which
     /// haven't actually been mapped
     pub fn write_split_kmer(&mut self, mapped_pos: usize, mapped_chrom: usize, base: u8) {
-        if mapped_chrom > self.curr_chrom {
+        while mapped_chrom > self.curr_chrom {
             self.fill_contig();
         }
         // Ambiguous bases may clash with the flanks, which are copied from