version 1.0.1 release

Kelly-ST-HRI · Mar 11, 2022 · 8ffb8a7 · 8ffb8a7
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diff --git a/README.md b/README.md
@@ -21,7 +21,7 @@ Contact:
 Contact the software author to discuss the software, report bugs or suggest enhancements at:
 https://github.com/StevenWingett/HiCUP/issues
 
-HiCUP+ (v1.0.0) maintainer: S. Thomas Kelly
+HiCUP+ (v1.0.1) maintainer: S. Thomas Kelly
 
 Contact:
 [email protected]
@@ -53,4 +53,4 @@ HiCUP Publication:
 
 Please cite the original version in addition to the updated software release:
 
-**Kelly, ST, et al. (2022) HiCUP+: a fast open-source pipeline for accurately processing large scale Hi-C sequence data. Software release v1.0.0 URL: https://github.com/hugp-ri/hicup-plus/**
+**Kelly, ST, et al. (2022) HiCUP+: a fast open-source pipeline for accurately processing large scale Hi-C sequence data. Software release v1.0.1 URL: https://github.com/hugp-ri/hicup-plus/**
diff --git a/README.txt b/README.txt
@@ -21,7 +21,7 @@ Contact:
 Contact the software author to discuss the software, report bugs or suggest enhancements at:
 https://github.com/StevenWingett/HiCUP/issues
 
-HiCUP+ (v1.0.0) maintainer: S. Thomas Kelly
+HiCUP+ (v1.0.1) maintainer: S. Thomas Kelly
 
 Contact:
 [email protected]
@@ -53,4 +53,4 @@ HiCUP Publication:
 
 Please cite the original version in addition to the updated software release:
 
-**Kelly, ST, et al. (2022) HiCUP+: a fast open-source pipeline for accurately processing large scale Hi-C sequence data. Software release v1.0.0 URL: https://github.com/hugp-ri/hicup-plus/**
+**Kelly, ST, et al. (2022) HiCUP+: a fast open-source pipeline for accurately processing large scale Hi-C sequence data. Software release v1.0.1 URL: https://github.com/hugp-ri/hicup-plus/**
diff --git a/RELEASE_NOTES.txt b/RELEASE_NOTES.txt
@@ -1,4 +1,21 @@
+RELEASE NOTES FOR HICUP-Plus v1.0.1 (11 MARCH 2022)
+
+-------------------------------------------------
+
+HiCUP+ v1.0.1 is a mnior update incorporating the changes described below:
+
+- implements built-in timing reported to stdout
+
+- bug fixes to post-processing in pairing step of hicup_mapper:
+ensures that reads are not sorted in intermeidiate SAM files
+and that reads are correctly paired in order. Index numbers
+are used for Bowtie, Bowtie2, and HiSAT2 in stream inputs.
+Matching strings in Dragen output is implemented without
+assuming FASTQ header format.
+
+
 RELEASE NOTES FOR HICUP-Plus v1.0.0 (15 FEBRUARY 2022)
+
 -------------------------------------------------
 
 HiCUP+ v1.0.0 is a major update incorporating the changes described below:

diff --git a/docs/index.rst b/docs/index.rst
@@ -951,6 +951,6 @@ Wingett S, *et al.* (2015) HiCUP: pipeline for mapping and processing Hi-C data.
 
 Please cite the original version in addition to the updated software release:
 
-Kelly, ST, *et al.* (2022) HiCUP+: a fast open-source pipeline for accurately processing large scale Hi-C sequence data. Software release v1.0.0 URL: `https://github.com/hugp-ri/hicup-plus/
+Kelly, ST, *et al.* (2022) HiCUP+: a fast open-source pipeline for accurately processing large scale Hi-C sequence data. Software release v1.0.1 URL: `https://github.com/hugp-ri/hicup-plus/
 <https://github.com/hugp-ri/hicup-plus/>`_
 
diff --git 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 = "1.0.0";
+our $VERSION = "1.0.1";
 
 use Data::Dumper;
 use strict;