Merge branch 'hotfix/5.3.5'

CHANGES.md

@@ -1,174 +1,232 @@
 # CHANGES
 
-## v5.3.4 
+## v5.3.5
+* Update `samtols` and `hstlib` to v1.7
+* Update `Bio::DB::HTS` to v2.10
+* Change tabix->query call to tabix->query_full
+* fixed bug in accessing chr prefixed chromosome names for HDR regions
+
+## v5.3.4
 * corrected typo in setup.sh removed safelist branches from .travis
 * Added checks for INST_METHOD
 * Changed CHANGES.md syntax to markdown linter
-* Exonerate install is now skipped if INST_METHOD is 2 
+* Exonerate install is now skipped if INST_METHOD is 2
+
+## v5.3.2
 
-## v5.3.2 
-* Fixed bug which caused incorrent assignment of mutant reads overlapping deletion regions to Unknon category - if there is any mismatch in 3prime region from deletionstart site 
+* Fixed bug which caused incorrent assignment of mutant reads overlapping deletion regions to Unknon category - if there is any mismatch in 3prime region from deletionstart site
+
+## v5.2.2
 
-## v5.2.2 
 * Heade line for SAMPLE is now generated from command line
 * Fixed bug for missing header data when running with bedonly option
 
-## v5.2.1 
+## v5.2.1
+
 * added condition to test vcf extension when bed file is not present
 
-## v5.2.0 
+## v5.2.0
+
 * added functionality to process bed file per chromosome
 * progress file check during concatenation step ignores already processed chromosomes
 * vcf file extension is optional if --bedOnly option is selected
 
-## v5.1.3 
+## v5.1.3
+
 * Fixed broken INFO tags in vcf and tsv
 * tags -t option is now only applicable to tsv file
-
-## v5.1.2 
+
+## v5.1.2
+
 * forced default shell to bash for syste command
 
-## v5.1.1 
+## v5.1.1
+
 * Added custom sorting for vcf files
 
-## v5.1.0 
+## v5.1.0
+
 * User can now run per chromosome analysis [useful to run in parallel ] and concatenate the resulting files
 
-## v5.0.0 
+## v5.0.0
+
 * Removed exonerate parameter to filter alignments based on score
 * Removed condition to discard alignment length smaller than read length
-* Added user defined option to specify exonerat percent value  
+* Added user defined option to specify exonerat percent value
 * Increased padding to extended reference sequence -- this will allow to map longer reads in amplicon data.
 
-## v4.5.6 
+## v4.5.6
+
 * Update to Bio::DB::HTS install to use already installed htslib
 
-## v4.5.5 
+## v4.5.5
+
 * updated version tag
 
-## v4.5.4 
+## v4.5.4
+
 * Removed default high depth regions filter option, users can optionally provide this file on command line (refer wiki)
 
 ## v4.5.3 * Updated licensing policy
+
 * Added option to supply external ignore depth file
 * removed legacy code to run external commands
 * Added prerelease.sh to
 
-## v4.5.2 
+## v4.5.2
+
 * Updated .gitignore to allow test data to be added to git
 
-## v4.5.1 
+## v4.5.1
+
 * Updated test data set files
 
-## v4.5.0 
+## v4.5.0
+
 * Added option to restrict reads based on mapping quality threshold
 
-## v4.4.2 
+## v4.4.2
+
 * Exonerate --percent threshold reduced to 90 from 95 to allow 4 mismatches
 
-## v4.4.1 
+## v4.4.1
+
 * More robust check for mismatches at varinat positions in the alignment
 
-## v4.4.0 
+## v4.4.0
+
 * added additional condition to check mismatch at the variant region in the alignment
 * reads mapping on alternate sequence and have mismatch at variant region were categorised into UNK [ unknown ] reads
 * updated option to correctly read bed file
 
-## v4.3.6 
+## v4.3.6
+
 * Creates augmented vcf file even if no records were augmented
 * Corrected processlog in vcf output header
 
-## v4.3.5 
+## v4.3.5
+
 * Minor change to test script
 
-## v4.3.4 
+## v4.3.4
+
 * Appropriate warning message when no vcf file found for a sample
 
-## v4.3.3 
+## v4.3.3
+
 * updated changes.md and verision information
 
-## V4.3.2 
+## V4.3.2
+
 * corrected tabix syntax as for Bio::DB::HTS::Tabix, added test for high depth region overlap
 
-## V4.3.1 
+## V4.3.1
+
 * removed legacy script from Makefile
 
-## V4.3.0 
+## V4.3.0
+
 * removed database dependecy code for external release
 
-## V4.2.3 
+## V4.2.3
+
 * replaced Tabix with Bio::DB::HTS::Tabix
 
-## V4.2.2 
+## V4.2.2
+
 * changed Bio::DB::HTS version to 1.12
 
-## V4.2.1 
+## V4.2.1
+
 * changed Bio::DB::HTS version to 1.11
 
-## V4.2.0 
+## V4.2.0
+
 * Added support to Bio::DB::HTS
 
-## V4.1.17 
+## V4.1.17
+
 * Updated SQL query to get input data to generate commands
 
-## V4.1.16 
+## V4.1.16
+
 * corrected condition to get unmatched normal
 
-## V4.1.15 
+## V4.1.15
+
 * Fixed vcf header, as it was copied twice in the outfile
 
-## V4.1.14 
+## V4.1.14
+
 * Added explicit check for normal sample using SIP_ATTRIBUTES table
 
-## V4.1.13 
+## V4.1.13
+
 * updated defualt project ini folder to cgpVaf
 
-## V4.1.12 
+## V4.1.12
+
 * Updated verison
 
-## V4.1.11 
+## V4.1.11
+
 * Added condition to ignore writing progress file if augment only option is selected
 
-## V4.1.10 
+## V4.1.10
+
 * Improved and corrected setup.sh and location of Makefile.PL
 
-## V4.1.8 
+## V4.1.8
+
 *added test to check final result removal
 *chnaged bio:db:sam version to 1.42
 
-## V4.1.7 
+## V4.1.7
+
 *changed installation path to bin from perl/bin in setup.sh
 
-## V4.1.6 
+## V4.1.6
+
 *fixed test to created progress file path
 
-## V4.1.5 
+## V4.1.5
+
 *updated condition to create outfile only if it is absent
 
-## V4.1.4 
+## V4.1.4
+
 *updated file postfix to <varinat>_vaf
 
-## V4.1.3 
+## V4.1.3
+
 *Added tumour sample name as postfix to tmp folder
 
-## V4.1.2 
+## V4.1.2
+
 *Added setup.sh
 
-## V4.1.1 
+## V4.1.1
+
 *Fixed bug in unmapped mate retrival
 
-## V4.1.0 
+## V4.1.0
+
 *Added option to accept vcf file as command line input
 
-## V4.0.1 
+## V4.0.1
+
 * Fixed readme file
 
-## V4.0 
+## V4.0
+
 * Contains pre-calculated VAF values in FORMAT field
 * Per chromosome progress tracking i.e., failed jobs can be resumed from last unsuccessful chromosome
 * Added setup script script
 
-## 3.2.4 
+## 3.2.4
+
 * Added condition to check snps that fall at the end of chromosome
 
-## 3.2.3 *	Added option to create config file for user defined list of samples
+## 3.2.3
+
+*	Added option to create config file for user defined list of samples

perl/Makefile.PL

@@ -28,7 +28,7 @@ WriteMakefile(
   EXE_FILES     => [qw( bin/cgpVaf.pl )],
   PREREQ_PM     => {
                     'Attribute::Abstract' => '1.02',
-                    'Bio::DB::HTS' => '1.12',
+                    'Bio::DB::HTS' => '2.10',
                     'Bio::Root::Version' => '1.006924',
                     'Capture::Tiny' => '0.24',
                     'Config::IniFiles' => '2.83',

perl/lib/Sanger/CGP/Vaf.pm

@@ -2,7 +2,7 @@ package Sanger::CGP::Vaf;
 use strict;
 use Const::Fast qw(const);
 
-our $VERSION = '5.3.4';
+our $VERSION = '5.3.5';
 
 const my $LICENSE =>
 "#################
@@ -16,4 +16,3 @@ sub license {
 }
 
 1;
-