From b2f17948fe4d88a6946e1c1c0aa5b789bd8a657a Mon Sep 17 00:00:00 2001
From: Simon Thomas Kelly <simonthomas.kelly@hugp.com>
Date: Wed, 8 Nov 2023 10:33:53 +0900
Subject: [PATCH] version 1.0.3 release

---
 README.md         |  6 +++---
 README.txt        |  6 +++---
 RELEASE_NOTES.txt | 12 ++++++++++++
 hicup_mapper      | 14 +++++++-------
 hicup_module.pm   |  2 +-
 5 files changed, 26 insertions(+), 14 deletions(-)

diff --git a/README.md b/README.md
index f566a3a..c25a028 100644
--- a/README.md
+++ b/README.md
@@ -54,7 +54,7 @@ Contact:
 Contact the software author to discuss the software, report bugs or suggest enhancements at:
 https://github.com/StevenWingett/HiCUP/issues
 
-HiCUP+ (v1.0.2) maintainer: S. Thomas Kelly
+HiCUP+ (v1.0.3) maintainer: S. Thomas Kelly
 
 Contact:
 simonthomas.kelly [at] hugp [dot] com
@@ -116,7 +116,7 @@ BibTeX version:
 The software release can be cited as follows:
 
 > Kelly, S. T. & Yuhara, S. (2022) HiCUP+: a fast open-source pipeline for accurately processing large scale Hi-C sequence data.
-> Software release v1.0.2 URL: [https://github.com/hugp-ri/hicup-plus/](https://github.com/hugp-ri/hicup-plus/)
+> Software release v1.0.3 URL: [https://github.com/hugp-ri/hicup-plus/](https://github.com/hugp-ri/hicup-plus/)
 
 BibTex version:
 
@@ -125,7 +125,7 @@ BibTex version:
     author = {Kelly, S. Thomas and Yuhara, Satoshi},
     title = {{H}i{C}{U}{P}-{P}lus: a fast open-source pipeline for accurately processing large scale {H}i-{C} sequence data}},
     year = {2022},
-    note = {Software release version v1.0.2},
+    note = {Software release version v1.0.3},
     url = {[https://github.com/hugp-ri/hicup-plus/](https://github.com/hugp-ri/hicup-plus/)},
 }
 ```
diff --git a/README.txt b/README.txt
index f566a3a..c25a028 100644
--- a/README.txt
+++ b/README.txt
@@ -54,7 +54,7 @@ Contact:
 Contact the software author to discuss the software, report bugs or suggest enhancements at:
 https://github.com/StevenWingett/HiCUP/issues
 
-HiCUP+ (v1.0.2) maintainer: S. Thomas Kelly
+HiCUP+ (v1.0.3) maintainer: S. Thomas Kelly
 
 Contact:
 simonthomas.kelly [at] hugp [dot] com
@@ -116,7 +116,7 @@ BibTeX version:
 The software release can be cited as follows:
 
 > Kelly, S. T. & Yuhara, S. (2022) HiCUP+: a fast open-source pipeline for accurately processing large scale Hi-C sequence data.
-> Software release v1.0.2 URL: [https://github.com/hugp-ri/hicup-plus/](https://github.com/hugp-ri/hicup-plus/)
+> Software release v1.0.3 URL: [https://github.com/hugp-ri/hicup-plus/](https://github.com/hugp-ri/hicup-plus/)
 
 BibTex version:
 
@@ -125,7 +125,7 @@ BibTex version:
     author = {Kelly, S. Thomas and Yuhara, Satoshi},
     title = {{H}i{C}{U}{P}-{P}lus: a fast open-source pipeline for accurately processing large scale {H}i-{C} sequence data}},
     year = {2022},
-    note = {Software release version v1.0.2},
+    note = {Software release version v1.0.3},
     url = {[https://github.com/hugp-ri/hicup-plus/](https://github.com/hugp-ri/hicup-plus/)},
 }
 ```
diff --git a/RELEASE_NOTES.txt b/RELEASE_NOTES.txt
index 33befe0..18d38ba 100644
--- a/RELEASE_NOTES.txt
+++ b/RELEASE_NOTES.txt
@@ -1,3 +1,15 @@
+RELEASE NOTES FOR HICUP-Plus v1.0.3 (8 NOVEMBER 2023)
+
+HiCUP+ v1.0.3 is a mnior update incorporating the changes described below:
+
+- adds support for the STAR aligner
+
+- updated logs for reporting results
+
+- updated documentation to describe supported aligners and Docker images
+
+-------------------------------------------------
+
 
 RELEASE NOTES FOR HICUP-Plus v1.0.2 (2 NOVEMBER 2022)
 
diff --git a/hicup_mapper b/hicup_mapper
index 3502957..f523610 100755
--- a/hicup_mapper
+++ b/hicup_mapper
@@ -662,17 +662,17 @@ sub map_file {
         $reads_processed += $too_short_to_map unless $config{dragen};
     }
 
-    #if ($reads_processed) {
-    #    $percent_too_short_to_map = sprintf( "%.1f", ( $too_short_to_map / $reads_processed * 100 ) );
-    #    $percent_unique           = sprintf( "%.1f", ( $unique_map / $reads_processed * 100 ) );
-    #    $percent_unmapped         = sprintf( "%.1f", ( $unmapped / $reads_processed * 100 ) );
-    #    $percent_multi            = sprintf( "%.1f", ( $multi_mapped / $reads_processed * 100 ) );
-    #} else {
+    if ($reads_processed) {
+        $percent_too_short_to_map = sprintf( "%.1f", ( $too_short_to_map / $reads_processed * 100 ) );
+        $percent_unique           = sprintf( "%.1f", ( $unique_map / $reads_processed * 100 ) );
+        $percent_unmapped         = sprintf( "%.1f", ( $unmapped / $reads_processed * 100 ) );
+        $percent_multi            = sprintf( "%.1f", ( $multi_mapped / $reads_processed * 100 ) );
+    } else {
         $percent_too_short_to_map = 'N/A';
         $percent_unique   = 'N/A';
         $percent_unmapped = 'N/A';
         $percent_multi    = 'N/A';
-    #}
+    }
 
     # reporting timing results   
     my $end2 = Time::HiRes::tv_interval($start_aligner);
diff --git a/hicup_module.pm b/hicup_module.pm
index 87dc138..700904f 100644
--- a/hicup_module.pm
+++ b/hicup_module.pm
@@ -8,7 +8,7 @@ our @EXPORT = qw(VERSION hasval deduplicate_array checkR process_config check_fi
 our @EXPORT_OK = qw(hashVal outdirFileNamer check_no_duplicate_filename check_filenames_ok 
     checkAligner checkAlignerIndices newopen quality_checker determineAlignerFormat get_csome_position);
 
-our $VERSION = "1.0.2";
+our $VERSION = "1.0.3";
 
 use Data::Dumper;
 use strict;