From 12431fc14fe02a584d013383088e8bd55d896db6 Mon Sep 17 00:00:00 2001 From: Steven Wingett Date: Tue, 15 Jan 2019 13:36:19 +0000 Subject: [PATCH] Fixed bug causing output files to not strictly adhere to SAM/BAM format. Prepared for next release. --- Conversion/hicup2fithic | 2 +- Conversion/hicup2gothic | 2 +- Conversion/hicup2hicpipe | 2 +- Conversion/hicup2homer | 2 +- Documentation/index.rst | 10 +++++----- RELEASE_NOTES.txt | 9 +++++++++ config_files/filter_example.conf | 2 +- config_files/hicup_example.conf | 2 +- hicup | 7 +++++-- hicup_deduplicator | 2 +- hicup_digester | 2 +- hicup_filter | 2 +- hicup_mapper | 2 +- hicup_module.pm | 4 ++-- hicup_truncater | 2 +- 15 files changed, 32 insertions(+), 20 deletions(-) diff --git a/Conversion/hicup2fithic b/Conversion/hicup2fithic index cf6c629..b25e656 100755 --- a/Conversion/hicup2fithic +++ b/Conversion/hicup2fithic @@ -12,7 +12,7 @@ use Data::Dumper; ################################################################################### ################################################################################### -##This file is Copyright (C) 2016, Steven Wingett (steven.wingett@babraham.ac.uk)## +##This file is Copyright (C) 2019, Steven Wingett (steven.wingett@babraham.ac.uk)## ## ## ## ## ##This file is part of HiCUP. ## diff --git a/Conversion/hicup2gothic b/Conversion/hicup2gothic index affe506..e0c0dcb 100755 --- a/Conversion/hicup2gothic +++ b/Conversion/hicup2gothic @@ -9,7 +9,7 @@ use hicup_module; ################################################################################### ################################################################################### -##This file is Copyright (C) 2016, Steven Wingett (steven.wingett@babraham.ac.uk)## +##This file is Copyright (C) 2019, Steven Wingett (steven.wingett@babraham.ac.uk)## ## ## ## ## ##This file is part of HiCUP. ## diff --git a/Conversion/hicup2hicpipe b/Conversion/hicup2hicpipe index 55d0deb..4abcffe 100755 --- a/Conversion/hicup2hicpipe +++ b/Conversion/hicup2hicpipe @@ -9,7 +9,7 @@ use hicup_module; ################################################################################### ################################################################################### -##This file is Copyright (C) 2016, Steven Wingett (steven.wingett@babraham.ac.uk)## +##This file is Copyright (C) 2019, Steven Wingett (steven.wingett@babraham.ac.uk)## ## ## ## ## ##This file is part of HiCUP. ## diff --git a/Conversion/hicup2homer b/Conversion/hicup2homer index e504965..d3ba809 100755 --- a/Conversion/hicup2homer +++ b/Conversion/hicup2homer @@ -9,7 +9,7 @@ use hicup_module; ################################################################################### ################################################################################### -##This file is Copyright (C) 2016, Steven Wingett (steven.wingett@babraham.ac.uk)## +##This file is Copyright (C) 2019, Steven Wingett (steven.wingett@babraham.ac.uk)## ## ## ## ## ##This file is part of HiCUP. ## diff --git a/Documentation/index.rst b/Documentation/index.rst index f9eb8a6..a4b6864 100644 --- 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 index 94e9762..ba660b4 100644 --- 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 index c4a7127..066d464 100644 --- 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 index 5c39589..9447d86 100644 --- 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 index 03a5e28..da5f8ec 100755 --- a/hicup +++ b/hicup @@ -16,7 +16,7 @@ use Data::Dumper; ################################################################################### ################################################################################### -##This file is Copyright (C) 2018, Steven Wingett (steven.wingett@babraham.ac.uk)## +##This file is Copyright (C) 2019, Steven Wingett (steven.wingett@babraham.ac.uk)## ## ## ## ## ##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 index 88e454c..0a69609 100755 --- a/hicup_deduplicator +++ b/hicup_deduplicator @@ -14,7 +14,7 @@ use Data::Dumper; ################################################################################### ################################################################################### -##This file is Copyright (C) 2018, Steven Wingett (steven.wingett@babraham.ac.uk)## +##This file is Copyright (C) 2019, Steven Wingett (steven.wingett@babraham.ac.uk)## ## ## ## ## ##This file is part of HiCUP. ## diff --git a/hicup_digester b/hicup_digester index 9699cd6..d021966 100755 --- a/hicup_digester +++ b/hicup_digester @@ -12,7 +12,7 @@ use Data::Dumper; ################################################################################### ################################################################################### -##This file is Copyright (C) 2018, Steven Wingett (steven.wingett@babraham.ac.uk)## +##This file is Copyright (C) 2019, Steven Wingett (steven.wingett@babraham.ac.uk)## ## ## ## ## ##This file is part of HiCUP. ## diff --git a/hicup_filter b/hicup_filter index ce9aebb..f553740 100755 --- a/hicup_filter +++ b/hicup_filter @@ -15,7 +15,7 @@ use Data::Dumper; ################################################################################### ################################################################################### -##This file is Copyright (C) 2018, Steven Wingett (steven.wingett@babraham.ac.uk)## +##This file is Copyright (C) 2019, Steven Wingett (steven.wingett@babraham.ac.uk)## ## ## ## ## ##This file is part of HiCUP. ## diff --git a/hicup_mapper b/hicup_mapper index db763d7..b8d508b 100755 --- a/hicup_mapper +++ b/hicup_mapper @@ -18,7 +18,7 @@ use Data::Dumper; ################################################################################### ################################################################################### -##This file is Copyright (C) 2018, Steven Wingett (steven.wingett@babraham.ac.uk)## +##This file is Copyright (C) 2019, Steven Wingett (steven.wingett@babraham.ac.uk)## ## ## ## ## ##This file is part of HiCUP. ## diff --git a/hicup_module.pm b/hicup_module.pm index e128381..8f2b241 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); -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 (steven.wingett@babraham.ac.uk)## +##This file is Copyright (C) 2019, Steven Wingett (steven.wingett@babraham.ac.uk)## ## ## ## ## ##This file is part of HiCUP. ## diff --git a/hicup_truncater b/hicup_truncater index e6c91c2..5761fa3 100755 --- a/hicup_truncater +++ b/hicup_truncater @@ -13,7 +13,7 @@ use Data::Dumper; ################################################################################### ################################################################################### -##This file is Copyright (C) 2018, Steven Wingett (steven.wingett@babraham.ac.uk)## +##This file is Copyright (C) 2019, Steven Wingett (steven.wingett@babraham.ac.uk)## ## ## ## ## ##This file is part of HiCUP. ##