From 4a9e694c024568ce7eb88f0e474a0d1ffb09f5af Mon Sep 17 00:00:00 2001
From: "Richard C. Burhans" <rico@bx.psu.edu>
Date: Wed, 11 Dec 2024 14:28:38 -0500
Subject: [PATCH 1/3] fixing mapped-reads symlinks

---
 tools/halfdeep/halfdeep.xml | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/tools/halfdeep/halfdeep.xml b/tools/halfdeep/halfdeep.xml
index be55c582957..f6dc230a2b4 100644
--- a/tools/halfdeep/halfdeep.xml
+++ b/tools/halfdeep/halfdeep.xml
@@ -30,9 +30,9 @@
         ## mapped reads
         ##
         #if $mapped_reads
-            ln -s '$mapped_reads' 'halfdeep/ref/mapped_reads/${reads_base}.bam' &&
-            ln -s '${reads_base}.bam' 'halfdeep/ref/mapped_reads/${reads_base}.sort.bam' &&
-            ln -s '$mapped_reads.metadata.bam_index' 'halfdeep/ref/mapped_reads/${reads_base}.sort.bam.bai' &&
+            ln -s '$mapped_reads' 'halfdeep/ref/mapped_reads/${reads_base}${reads.ext}.bam' &&
+            ln -s '${reads_base}.bam' 'halfdeep/ref/mapped_reads/${reads_base}${reads.ext}.sort.bam' &&
+            ln -s '$mapped_reads.metadata.bam_index' 'halfdeep/ref/mapped_reads/${reads_base}{reads.ext}.sort.bam.bai' &&
         #end if
         ##
         ## run bam_depth.sh

From 602a06383ae8f3cc3bcdd6a6fb47f786c6f4ff84 Mon Sep 17 00:00:00 2001
From: "Richard C. Burhans" <rico@bx.psu.edu>
Date: Wed, 11 Dec 2024 14:32:47 -0500
Subject: [PATCH 2/3] fixed another mapped-read symlink

---
 tools/halfdeep/halfdeep.xml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tools/halfdeep/halfdeep.xml b/tools/halfdeep/halfdeep.xml
index f6dc230a2b4..d6da4d790c6 100644
--- a/tools/halfdeep/halfdeep.xml
+++ b/tools/halfdeep/halfdeep.xml
@@ -31,7 +31,7 @@
         ##
         #if $mapped_reads
             ln -s '$mapped_reads' 'halfdeep/ref/mapped_reads/${reads_base}${reads.ext}.bam' &&
-            ln -s '${reads_base}.bam' 'halfdeep/ref/mapped_reads/${reads_base}${reads.ext}.sort.bam' &&
+            ln -s '${reads_base}${reads.ext}.bam' 'halfdeep/ref/mapped_reads/${reads_base}${reads.ext}.sort.bam' &&
             ln -s '$mapped_reads.metadata.bam_index' 'halfdeep/ref/mapped_reads/${reads_base}{reads.ext}.sort.bam.bai' &&
         #end if
         ##

From cfa6bb8667455a8f7246c3fef165d6badcbc81fd Mon Sep 17 00:00:00 2001
From: "Richard C. Burhans" <rico@bx.psu.edu>
Date: Wed, 11 Dec 2024 14:33:16 -0500
Subject: [PATCH 3/3] bumping suffix

---
 tools/halfdeep/macros.xml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tools/halfdeep/macros.xml b/tools/halfdeep/macros.xml
index 25ef5b7322d..536f15b4d8e 100644
--- a/tools/halfdeep/macros.xml
+++ b/tools/halfdeep/macros.xml
@@ -5,7 +5,7 @@
         </requirements>
     </xml>
     <token name="@TOOL_VERSION@">0.1.0</token>
-    <token name="@VERSION_SUFFIX@">0</token>
+    <token name="@VERSION_SUFFIX@">1</token>
     <token name="@PROFILE@">21.05</token>
     <xml name="citations">
         <citations>