Fixed bug causing output files to not strictly adhere to SAM/BAM form…

…at. Prepared for next release.
StevenWingett · Jan 15, 2019 · 12431fc · 12431fc
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commit 12431fc
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Showing 15 changed files with 32 additions and 20 deletions.
diff --git a/Conversion/hicup2fithic b/Conversion/hicup2fithic
@@ -12,7 +12,7 @@ use Data::Dumper;
 
 ###################################################################################
 ###################################################################################
-##This file is Copyright (C) 2016, Steven Wingett ([email protected])##
+##This file is Copyright (C) 2019, Steven Wingett ([email protected])##
 ##                                                                               ##
 ##                                                                               ##
 ##This file is part of HiCUP.                                                    ##

diff --git a/Conversion/hicup2gothic b/Conversion/hicup2gothic
@@ -9,7 +9,7 @@ use hicup_module;
 
 ###################################################################################
 ###################################################################################
-##This file is Copyright (C) 2016, Steven Wingett ([email protected])##
+##This file is Copyright (C) 2019, Steven Wingett ([email protected])##
 ##                                                                               ##
 ##                                                                               ##
 ##This file is part of HiCUP.                                                    ##

diff --git a/Conversion/hicup2hicpipe b/Conversion/hicup2hicpipe
@@ -9,7 +9,7 @@ use hicup_module;
 
 ###################################################################################
 ###################################################################################
-##This file is Copyright (C) 2016, Steven Wingett ([email protected])##
+##This file is Copyright (C) 2019, Steven Wingett ([email protected])##
 ##                                                                               ##
 ##                                                                               ##
 ##This file is part of HiCUP.                                                    ##

diff --git a/Conversion/hicup2homer b/Conversion/hicup2homer
@@ -9,7 +9,7 @@ use hicup_module;
 
 ###################################################################################
 ###################################################################################
-##This file is Copyright (C) 2016, Steven Wingett ([email protected])##
+##This file is Copyright (C) 2019, Steven Wingett ([email protected])##
 ##                                                                               ##
 ##                                                                               ##
 ##This file is part of HiCUP.                                                    ##

diff --git a/Documentation/index.rst b/Documentation/index.rst
@@ -170,7 +170,7 @@ Use a text editor to edit the configuration file as required, such as in the fol
     Longest: 700
 
     #Minimum di-tag length (optional parameter)
-    Shortest: 100
+    Shortest: 50
 
     #FASTQ files to be analysed, placing paired files on adjacent lines
     s_1_1_sequence.txt
@@ -263,10 +263,10 @@ The designated configuration file sets the parameters for the whole pipeline. Th
     Format: Sanger 
 
     #Maximum di-tag length (optional parameter)
-    Longest: 800
+    Longest: 700
 
     #Minimum di-tag length (optional parameter)
-    Shortest: 150
+    Shortest: 50
 
     #FASTQ files to be analysed, placing paired files on adjacent lines
     s_1_1_sequence.txt
@@ -721,8 +721,8 @@ Example command:
     Index: [Path to Bowtie/Bowtie2 indices on your system]
     R: [Path to R on your system]
     Format: phred33-quals
-    Shortest: 150
-    Longest: 800
+    Shortest: 50
+    Longest: 700
     test_dataset1.fastq
     test_dataset2.fastq
 

diff --git a/RELEASE_NOTES.txt b/RELEASE_NOTES.txt
@@ -1,3 +1,12 @@
+RELEASE NOTES FOR HICUP V0.7.2 (15 January 2018)
+------------------------------------------------
+
+HiCUP v0.7.2 is a minor update incorporating the changes described below:
+
+-Fixed bug causing output files to not strictly adhere to SAM/BAM format. 
+
+
+
 RELEASE NOTES FOR HICUP V0.7.1 (12 November 2018)
 -------------------------------------------------
 

diff --git a/config_files/filter_example.conf b/config_files/filter_example.conf
@@ -22,7 +22,7 @@ Digest: Digest_human7_HindIII_None_15-42-00_14-08-2013.txt
 
 
 #Minimum allowable di-tag size (optional) 
-Shortest: 100
+Shortest: 50
 
 
 #Maximum allowable di-tag size (optional)

diff --git a/config_files/hicup_example.conf b/config_files/hicup_example.conf
@@ -50,7 +50,7 @@ Longest: 700
 
 
 #Minimum di-tag length (optional parameter)
-Shortest: 100
+Shortest: 50
 
 
 #FASTQ files to be analysed, placing paired files on adjacent lines

diff --git a/hicup b/hicup
@@ -16,7 +16,7 @@ use Data::Dumper;
 
 ###################################################################################
 ###################################################################################
-##This file is Copyright (C) 2018, Steven Wingett ([email protected])##
+##This file is Copyright (C) 2019, Steven Wingett ([email protected])##
 ##                                                                               ##
 ##                                                                               ##
 ##This file is part of HiCUP.                                                    ##
@@ -331,7 +331,10 @@ if ( $config{zip} ) {
 #Map and pair sequences
 my $ligation = "\@PG\tID:HiCUP Truncater\tVN:" . $hicup_module::VERSION;       #Create the hidden ligation flag to send to HiCUP mapper to print the hicup_truncation settings to the output file
 if ( $config{re1} ) {
-    $ligation = $ligation . "\tDS:\"" . "$config{re1}\"";
+	#We cannot have a ":" in the SAM header at this point, so remove it
+	my $colonless_re1 = $config{re1};
+	$colonless_re1 =~ s/://g;
+    $ligation = $ligation . "\tDS:\"" . "$colonless_re1\"";
 } else {
     $ligation = $ligation . "\tDS\"" . "Ligation junction sequences $config{sequence}\"";
 }

diff --git a/hicup_deduplicator b/hicup_deduplicator
@@ -14,7 +14,7 @@ use Data::Dumper;
 
 ###################################################################################
 ###################################################################################
-##This file is Copyright (C) 2018, Steven Wingett ([email protected])##
+##This file is Copyright (C) 2019, Steven Wingett ([email protected])##
 ##                                                                               ##
 ##                                                                               ##
 ##This file is part of HiCUP.                                                    ##

diff --git a/hicup_digester b/hicup_digester
@@ -12,7 +12,7 @@ use Data::Dumper;
 
 ###################################################################################
 ###################################################################################
-##This file is Copyright (C) 2018, Steven Wingett ([email protected])##
+##This file is Copyright (C) 2019, Steven Wingett ([email protected])##
 ##                                                                               ##
 ##                                                                               ##
 ##This file is part of HiCUP.                                                    ##

diff --git a/hicup_filter b/hicup_filter
@@ -15,7 +15,7 @@ use Data::Dumper;
 
 ###################################################################################
 ###################################################################################
-##This file is Copyright (C) 2018, Steven Wingett ([email protected])##
+##This file is Copyright (C) 2019, Steven Wingett ([email protected])##
 ##                                                                               ##
 ##                                                                               ##
 ##This file is part of HiCUP.                                                    ##

diff --git a/hicup_mapper b/hicup_mapper
@@ -18,7 +18,7 @@ use Data::Dumper;
 
 ###################################################################################
 ###################################################################################
-##This file is Copyright (C) 2018, Steven Wingett ([email protected])##
+##This file is Copyright (C) 2019, Steven Wingett ([email protected])##
 ##                                                                               ##
 ##                                                                               ##
 ##This file is part of HiCUP.                                                    ##

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);
 
-our $VERSION = "0.7.1";
+our $VERSION = "0.7.2";
 
 use Data::Dumper;
 use strict;
@@ -19,7 +19,7 @@ use lib $Bin;
 
 ###################################################################################
 ###################################################################################
-##This file is Copyright (C) 2018, Steven Wingett ([email protected])##
+##This file is Copyright (C) 2019, Steven Wingett ([email protected])##
 ##                                                                               ##
 ##                                                                               ##
 ##This file is part of HiCUP.                                                    ##

diff --git a/hicup_truncater b/hicup_truncater
@@ -13,7 +13,7 @@ use Data::Dumper;
 
 ###################################################################################
 ###################################################################################
-##This file is Copyright (C) 2018, Steven Wingett ([email protected])##
+##This file is Copyright (C) 2019, Steven Wingett ([email protected])##
 ##                                                                               ##
 ##                                                                               ##
 ##This file is part of HiCUP.                                                    ##