From bb7e964d510757c93213bd5a0d2c08b040c5a3e2 Mon Sep 17 00:00:00 2001
From: Simon Thomas Kelly <simonthomas.kelly@hugp.com>
Date: Fri, 29 Oct 2021 17:03:38 +0900
Subject: [PATCH] force reads to short to map as zero

---
 hicup_mapper | 8 ++------
 1 file changed, 2 insertions(+), 6 deletions(-)

diff --git a/hicup_mapper b/hicup_mapper
index c9b67ba..0bdf329 100755
--- a/hicup_mapper
+++ b/hicup_mapper
@@ -407,7 +407,7 @@ sub map_file {
             $read .= scalar <INPUT>;
             $read .= scalar <INPUT>;
             if ( $read_length < 20 ) {    #Don't pass very short reads to Bowtie
-                $too_short_to_map++;
+                $too_short_to_map++ unless $config{dragen};
                 next;
             }
         } elsif (/^@/) {
@@ -545,11 +545,7 @@ sub map_file {
 
     if ( $config{dragen}) {
         #Reads processed is those reported by Dragen including those too short (unmapped)
-        if ( $too_short_to_map < $unmapped) {
-            $unmapped = $unmapped - $too_short_to_map
-        } else {
-            $too_short_to_map = 0;
-        }
+        $too_short_to_map = 0;
     }
     else {
         #Reads processed is the number of reads processed by Bowtie + those too short to send to Bowtie