Merge pull request #54 from StevenWingett/devel_capture

Devel capture
StevenWingett · Jul 13, 2021 · c6fb522 · c6fb522
2 parents 7b7720b + 731e5b7
commit c6fb522
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diff --git a/.gitignore b/.gitignore
@@ -1 +1,2 @@
 .DS_Store
+.vscode/
diff --git a/Documentation/index.rst b/Documentation/index.rst
@@ -771,6 +771,14 @@ Arima Protocol
 This is all that is additionally required to process an Arima Hi-C dataset.
 
 
+###############
+Miscellaneous Functioality
+###############
+The main HiCUP folder contains a folder named 'Misc' which contains several useful scripts.
+
+The script hicup_capture is for identifying di-tags mapping to captured regions of the genome in Capture Hi-C experiments (Capture Hi-C is described in - DOI: 10.1101/gr.185272.114).  For a di-tag to be considered captured, both or either read needs to map to a captured restriction fragment. 
+
+
 ##########
 References
 ##########

diff --git a/Misc/get_captured_reads → Misc/hicup_capture b/Misc/get_captured_reads → Misc/hicup_capture
@@ -4,13 +4,16 @@ use strict;
 use warnings;
 use Getopt::Long;
 use POSIX;
+use FindBin '$Bin';
+use lib "$Bin/../";
+use lib "$Bin/";    #For when hicup_module is in the same dir as this script
 use hicup_module;
 
 use Data::Dumper;
 
 ###################################################################################
 ###################################################################################
-##This file is Copyright (C) 2016, Steven Wingett ([email protected])##
+##This file is Copyright (C) 2020, Steven Wingett ([email protected])##
 ##                                                                               ##
 ##                                                                               ##
 ##This file is part of HiCUP.                                                    ##
@@ -56,12 +59,11 @@ if ( $config{help} ) {    #Print help and exit
 
 #Print version and exit
 if ( $config{version} ) {
-    print "HiCUP get_captured_reads v$hicup_module::VERSION\n";
+    print "HiCUP hicup_capture v$hicup_module::VERSION\n";
     exit(0);
 }
 
-
-print "Running get_captured_reads.pl v$hicup_module::VERSION\n";
+print "Running hicup_capture v$hicup_module::VERSION\n";
 
 ##############################################
 #Check input
@@ -506,26 +508,31 @@ __DATA__
 
 SYNOPSIS
 
-get_captured_reads.pl
+hicup_capture
 
-get_captured_reads.pl [OPTIONS] --baits [baits file] [BAM/SAM files]
-get_captured_reads.pl [OPTIONS]
+hicup_capture [OPTIONS] --baits [baits file] [BAM/SAM files]
+hicup_capture [OPTIONS]
 
 FUNCTION
 
-Takes a baits file and BAM/SAM Hi-C files (output from HiCUP) and separates 'captured'
-di-tags from 'uncaptured' di-tags, writing into two different BAM files. 
-Reports summary statistics on the results.
+For Capture Hi-C (CHiC) experiments. Takes a baits file and 
+BAM/SAM HiCUP file(s) and separates 'captured' di-tags from
+'uncaptured' di-tags, writing the output into two different 
+BAM files. Reports summary statistics on the results.
 
 The baits file should be a tab-delimited file of format:
 Chromosome    Start    End
  
 COMMAND LINE OPTIONS
 
 --baits            Baits format file
---header           Specify number of header lines in the baits file (i.e. skip these)
+--header           Specify number of header lines in the baits 
+                   file (i.e. skip these) [Default 0]
 --help             Print help message and exit
---interactions     Calculate interaction frequecies between baits
+--interactions     Calculate interaction frequecies between 
+                   baits
 --version          Print the program version and exit
 
-Steven Wingett, Babraham Institute, Cambridge, UK ([email protected])
+Steven Wingett
+Babraham Institute, Cambridge, UK
+The MRC Laboratory of Molecular Biology, Cambridge, UK
diff --git a/RELEASE_NOTES.txt b/RELEASE_NOTES.txt
@@ -1,9 +1,26 @@
+RELEASE NOTES FOR HICUP v0.8.2 (13 JULY 2021)
+-------------------------------------------------
+
+HiCUP v0.8.2 is a minor update incorporating the change described below:
+
+- The get_captured_reads script has been renamed to hicup_capture. The
+script is found in the Misc folder and is used to identify "captured"
+di-tags in a Capture Hi-C experiment.  The renamed script now works in
+both the Misc directory or in the same directory as hicup_module (which 
+is useful for Conda installs or when creating symbolic links to the 
+hicup_capture script).
+
+
+
 RELEASE NOTES FOR HICUP v0.8.1 (16 FEBRUARY 2021)
 -------------------------------------------------
 
 HiCUP v0.8.1 is a minor update incorporating the change described below:
 
-- HiCUP previously could not process Gzipped files when run on a Mac computer.  While HiCUP is designed for Linux systems, a simple fix was made on how Gzipped files are uncompressed and consequently HiCUP should now work on Mac systems.
+- HiCUP previously could not process Gzipped files when run on a Mac 
+computer.  While HiCUP is designed for Linux systems, a simple fix was 
+made on how Gzipped files are uncompressed and consequently HiCUP should 
+now work on Mac systems.
 
 
 

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 = "0.8.1";
+our $VERSION = "0.8.2";
 
 use Data::Dumper;
 use strict;