From c0d5cb8efd2d473bc92f0f956d5569fc7e420f41 Mon Sep 17 00:00:00 2001 From: Alexander Dilthey Date: Wed, 30 Oct 2019 19:51:54 +0100 Subject: [PATCH 01/33] Better error message --- HLA-LA.pl | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/HLA-LA.pl b/HLA-LA.pl index 8da05f7..2e00868 100755 --- a/HLA-LA.pl +++ b/HLA-LA.pl @@ -258,7 +258,7 @@ die "Incorrect header for $f ($#firstLine_fields vs $#expected_firstLine_fields)" unless($#firstLine_fields == $#expected_firstLine_fields); for(my $i = 0; $i <= $#firstLine_fields; $i++) { - die "Incorrect header for $f" unless($firstLine_fields[$i] eq $expected_firstLine_fields[$i]); + die "Incorrect header for $f - expect $expected_firstLine_fields[$i], got $firstLine_fields[$i]" unless($firstLine_fields[$i] eq $expected_firstLine_fields[$i]); } my $n_contigs = 0; From 78feac6b30ab6d1103de04e7b81cf5cf641fd3ff Mon Sep 17 00:00:00 2001 From: Alexander Dilthey Date: Wed, 30 Oct 2019 19:53:24 +0100 Subject: [PATCH 02/33] Add reference --- .../GRCh38.p12.genome.XY_idxstats.txt | 595 ++++++++++++++++++ 1 file changed, 595 insertions(+) create mode 100644 additionalReferences/PRG_MHC_GRCh38_withIMGT/GRCh38.p12.genome.XY_idxstats.txt diff --git a/additionalReferences/PRG_MHC_GRCh38_withIMGT/GRCh38.p12.genome.XY_idxstats.txt b/additionalReferences/PRG_MHC_GRCh38_withIMGT/GRCh38.p12.genome.XY_idxstats.txt new file mode 100644 index 0000000..89ce9f7 --- /dev/null +++ b/additionalReferences/PRG_MHC_GRCh38_withIMGT/GRCh38.p12.genome.XY_idxstats.txt @@ -0,0 +1,595 @@ +contigID contigLength ExtractCompleteContig PartialExtraction_Start PartialExtraction_Stop +chr1 248956422 0 +chr2 242193529 0 +chr3 198295559 0 +chr4 190214555 0 +chr5 181538259 0 +chr6 170805979 0 28510120 33480577 +chr7 159345973 0 +chr8 145138636 0 +chr9 138394717 0 +chr10 133797422 0 +chr11 135086622 0 +chr12 133275309 0 +chr13 114364328 0 +chr14 107043718 0 +chr15 101991189 0 +chr16 90338345 0 +chr17 83257441 0 +chr18 80373285 0 +chr19 58617616 0 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README.md --- README.md | 6 ++---- 1 file changed, 2 insertions(+), 4 deletions(-) diff --git a/README.md b/README.md index bca14cf..5449713 100644 --- a/README.md +++ b/README.md @@ -22,12 +22,10 @@ ## Basics -HLA\*LA carries out HLA typing based on a population reference graph and employs a new linear projection method to align reads to the graph. See this [preprint](https://www.biorxiv.org/content/early/2018/10/26/453555) and this [blog post](https://genomeinformatics.github.io/HLA-LA/). +HLA\*LA carries out HLA typing based on a population reference graph and employs a new linear projection method to align reads to the graph. See the [publication](https://academic.oup.com/bioinformatics/article/35/21/4394/5426702) and this [blog post](https://genomeinformatics.github.io/HLA-PRG-LA/). HLA\*LA is faster and less resource-intensive than HLA*PRG. -See [this blog post](https://genomeinformatics.github.io/HLA-LA/) for a description of the algorithm. - ## Installing HLA*LA ### Via bioconda ### @@ -214,4 +212,4 @@ Important: if you miss regions, the reads aligned to these are lost for the infe ## Citing HLA*LA -Please cite the [original HLA*PRG paper](http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1005151). +Please cite the [HLA\*LA publication](https://academic.oup.com/bioinformatics/article/35/21/4394/5426702). From 8cfdb78d64e849322c8ac8b6f01cfae5e5a1505f Mon Sep 17 00:00:00 2001 From: jafors Date: Mon, 2 Dec 2019 17:25:55 +0100 Subject: [PATCH 04/33] Possibility of using a user-defined graph directory --- HLA-LA.pl | 13 +++++++++++++ 1 file changed, 13 insertions(+) diff --git a/HLA-LA.pl b/HLA-LA.pl index 2e00868..c85fd67 100755 --- a/HLA-LA.pl +++ b/HLA-LA.pl @@ -16,6 +16,7 @@ my $_BAM; my $graph; +my $customGraphDir; my $sampleID; my $qsub; my $samtools_bin; @@ -32,6 +33,7 @@ GetOptions ( 'BAM:s' => \$_BAM, 'graph:s' => \$graph, + 'customGraphDir:s' => \$customGraphDir, 'sampleID:s' => \$sampleID, 'qsub:s' => \$qsub, 'workingDir:s' => \$workingDir_param, @@ -193,6 +195,12 @@ } my $full_graph_dir = $FindBin::RealBin . '/../graphs/' . $graph; +if ($customGraphDir and (-e $customGraphDir)) +{ + print "Using custom graph directory $customGraphDir\n"; + $full_graph_dir = $customGraphDir . '/' . $graph; +} + my $known_references_dir = $full_graph_dir . '/knownReferences'; unless(-e $full_graph_dir) { @@ -230,6 +238,11 @@ my @files_references = glob($known_references_dir . '/*.txt'); die "No known reference files in knownReferences ($full_graph_dir)?" unless(@files_references); my $additional_references_dir = $this_bin_dir . '/additionalReferences/' . $graph; +if ($customGraphDir and (-e $customGraphDir)) +{ + $additional_references_dir = $full_graph_dir . '/../additionalReferences/' . $graph; +} + if(-e $additional_references_dir) { my @additional_files_references = glob($additional_references_dir . '/*.txt'); From bed4ffd3914851b2b22f3aebb3423c42b74a6eeb Mon Sep 17 00:00:00 2001 From: jafors Date: Mon, 2 Dec 2019 17:28:08 +0100 Subject: [PATCH 05/33] Adding information which reference file is used to runtime terminal output --- HLA-LA.pl | 2 ++ 1 file changed, 2 insertions(+) diff --git a/HLA-LA.pl b/HLA-LA.pl index c85fd67..b94a032 100755 --- a/HLA-LA.pl +++ b/HLA-LA.pl @@ -334,6 +334,8 @@ my $compatible_reference_file = $compatible_files[0]; +print "Using $compatible_reference_file as reference file.\n"; + my @refIDs_for_extraction; foreach my $refID (@BAM_idx_contigOrder) { From fbc682a6349d9602d6e3bb6ae850bd17a37dffd9 Mon Sep 17 00:00:00 2001 From: Alexander Dilthey Date: Thu, 26 Dec 2019 17:58:08 +0100 Subject: [PATCH 06/33] Add missing file --- Perl/amendSecondaryAlignmentSequences.pl | 161 +++++++++++++++++++++++ 1 file changed, 161 insertions(+) create mode 100644 Perl/amendSecondaryAlignmentSequences.pl diff --git a/Perl/amendSecondaryAlignmentSequences.pl b/Perl/amendSecondaryAlignmentSequences.pl new file mode 100644 index 0000000..c99d83d --- /dev/null +++ b/Perl/amendSecondaryAlignmentSequences.pl @@ -0,0 +1,161 @@ +use strict; + +#!/usr/bin/env perl + +## Author: Alexander Dilthey (HHU/UKD, NHGRI-NIH), Evan Biederstedt (NYGC), Nathan Dunn (LBNL), Nancy Hansen (NIH), Aarti Jajoo (Baylor), Jeff Oliver (Arizona), Andrew Olsen (CSHL) +## License: The MIT License, https://github.com/NCBI-Hackathons/Graph_Genomes/blob/master/LICENSE + +use strict; +use warnings; +use Data::Dumper; +use Getopt::Long; +use List::Util qw/max all/; +use List::MoreUtils qw/mesh/; +use Bio::DB::HTS; + +$| = 1; + +## Usage: +## amendSecondaryAlignmentSequences.pl --input +## --output + +my $input; +my $output; + +GetOptions ( + 'input:s' => \$input, + 'output:s' => \$output, +); + +unless($input) +{ + die "Please specify --input (SAM file)"; +} + +unless($output) +{ + die "Please specify --output (SAM file)"; +} + +my $currentReadID; +my $currentReadSequence_positive; +my %processedReadIDs; +open(OUTPUT, '>', $output) or die "Cannot open $output"; +open(INPUT, '<', $input) or die "Cannot open $input"; +while() +{ + my $line = $_; + next unless($line); + if(substr($line, 0, 1) eq '@') + { + print OUTPUT $line; + } + else + { + my @line_fields = split(/\t/, $line); + die unless(scalar(@line_fields) >= 11); + my $Name = $line_fields[0]; + my $FLAG = $line_fields[1]; + my $rName = $line_fields[2]; + my $POS = $line_fields[3]; + my $mapQ = $line_fields[4]; + my $CIGAR = $line_fields[5]; + my $SEQ = $line_fields[9]; + my $QUAL = $line_fields[10]; + + if($SEQ eq '*') + { + die unless($currentReadID eq $Name); + my $currentReadSequence_rightStrand; + die "Read $Name line $. in $input, we apparently don't have a primary read sequence: $currentReadSequence_positive" unless(defined $currentReadSequence_positive); + if(isReverseComplemented($FLAG)) + { + $currentReadSequence_rightStrand = reverseComplement($currentReadSequence_positive); + } + else + { + $currentReadSequence_rightStrand = $currentReadSequence_positive; + } + + die unless($CIGAR =~ /^((\d+)H)?(.+?)((\d+)H)?$/); + my $hardclipping_left = $2; + my $hardclipping_right = $5; + my $middleComponent = $3; + die if($middleComponent =~ /H/i); + + $hardclipping_left = 0 unless($hardclipping_left); + $hardclipping_right = 0 unless($hardclipping_right); + + die "Weird hardclipping value: $hardclipping_left $CIGAR" unless($hardclipping_left =~ /^\d+$/); + die unless($hardclipping_right =~ /^\d+$/); + + substr($currentReadSequence_rightStrand, 0, $hardclipping_left) = ''; + substr($currentReadSequence_rightStrand, length($currentReadSequence_rightStrand) - $hardclipping_right, $hardclipping_right) = ''; + + die unless(length($currentReadSequence_rightStrand) == (length($currentReadSequence_positive) - $hardclipping_left - $hardclipping_right)); + + $line_fields[9] = $currentReadSequence_rightStrand; + + print OUTPUT join("\t", @line_fields); + } + else + { + print OUTPUT $line; + } + + if((not defined $currentReadID) or ($currentReadID ne $Name)) + { + die "Reads are not ordered by read ID" if($processedReadIDs{$Name}); + $processedReadIDs{$Name}++; + die unless(isPrimary($FLAG)); + die if($SEQ eq '*'); + die if($CIGAR =~ /H/); + if(isReverseComplemented($FLAG)) + { + die unless(defined $SEQ); + $currentReadSequence_positive = reverseComplement($SEQ); + } + else + { + $currentReadSequence_positive = $SEQ; + } + } + $currentReadID = $Name; + } + +} +close(INPUT); +close(OUTPUT); + +print "\n\nDone. Generated $output.\n\n"; + + +sub isReverseComplemented +{ + my $FLAG = shift; + die unless(defined $FLAG); + return ($FLAG & 16); +} + +sub isNotPrimary +{ + my $FLAG = shift; + die unless(defined $FLAG); + return ($FLAG & 256); +} + + +sub isPrimary +{ + my $FLAG = shift; + die unless(defined $FLAG); + return (! isNotPrimary($FLAG)); +} + +sub reverseComplement +{ + my $kMer = shift; + $kMer =~ tr/ACGT/TGCA/; + return reverse($kMer); + return $kMer; +} \ No newline at end of file From 24930adadb0d2b6bcd69a271401dfc88a5d09f4d Mon Sep 17 00:00:00 2001 From: Alexander Dilthey Date: Tue, 7 Jan 2020 20:16:03 +0100 Subject: [PATCH 07/33] Bugfix when not using minimap2 --- globalAlignment.pl | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/globalAlignment.pl b/globalAlignment.pl index ce07e36..f3b5103 100755 --- a/globalAlignment.pl +++ b/globalAlignment.pl @@ -74,7 +74,8 @@ my $fromBWA_mapping_fn_sam = $fromBWA_mapping_fn . '.sam'; my $fromBWA_mapping_fn_sam_amended = $fromBWA_mapping_fn . '.sam.amended'; #my $cmd_map = qq($bwa_bin mem -t 8 -a -x intractg $forBWA_ref_fn $query > $fromBWA_mapping_fn_sam); - my $cmd_map = qq($bwa_bin mem -a -x pacbio $forBWA_ref_fn $query | $samtools_bin view -Sb - > $fromBWA_mapping_fn); + #my $cmd_map = qq($bwa_bin mem -a -x pacbio $forBWA_ref_fn $query | $samtools_bin view -Sb - > $fromBWA_mapping_fn); + my $cmd_map = qq($bwa_bin mem -a -x pacbio $forBWA_ref_fn $query > $fromBWA_mapping_fn_sam); if($use_minimap2) { From f7b0ade99bf365c465621dc93a79b5b233c178ba Mon Sep 17 00:00:00 2001 From: jafors Date: Tue, 14 Jan 2020 15:45:12 +0100 Subject: [PATCH 08/33] Update from upstream master --- HLA-LA.pl | 25 +++++-------------------- 1 file changed, 5 insertions(+), 20 deletions(-) diff --git a/HLA-LA.pl b/HLA-LA.pl index b94a032..060a562 100755 --- a/HLA-LA.pl +++ b/HLA-LA.pl @@ -29,7 +29,6 @@ my $extractExonkMerCounts; my $longReads = 0; my $testing = 0; -my $samtools_T; GetOptions ( 'BAM:s' => \$_BAM, 'graph:s' => \$graph, @@ -46,7 +45,6 @@ 'extractExonkMerCounts:s' => \$extractExonkMerCounts, 'longReads:s' => \$longReads, 'testing:s' => \$testing, - 'samtools_T:s' => \$samtools_T, ); if ($extractExonkMerCounts) @@ -152,6 +150,7 @@ } my $working_dir_thisSample = $working_dir . '/' . $sampleID; + print "HLA-LA.pl\n\n"; print "Identified paths:\n"; @@ -200,7 +199,6 @@ print "Using custom graph directory $customGraphDir\n"; $full_graph_dir = $customGraphDir . '/' . $graph; } - my $known_references_dir = $full_graph_dir . '/knownReferences'; unless(-e $full_graph_dir) { @@ -211,11 +209,6 @@ die "Graph directory $full_graph_dir does not seem to be complete - does this directory specify a valid graph for HLA-LA?"; } -unless((-e $full_graph_dir . '/serializedGRAPH')) -{ - die "It seems that you have not yet indexed graph $graph - suggested command: ../bin/HLA-LA --action prepareGraph --PRG_graph_dir ../graphs/${graph}"; -} - # get index for this BAM my $command_idxstats = qq($samtools_bin idxstats $BAM); my $command_idxstats_output = `$command_idxstats`; @@ -240,9 +233,8 @@ my $additional_references_dir = $this_bin_dir . '/additionalReferences/' . $graph; if ($customGraphDir and (-e $customGraphDir)) { - $additional_references_dir = $full_graph_dir . '/../additionalReferences/' . $graph; + $additional_references_dir = $full_graph_dir . '/../additionalReferences/' . $graph; } - if(-e $additional_references_dir) { my @additional_files_references = glob($additional_references_dir . '/*.txt'); @@ -271,7 +263,7 @@ die "Incorrect header for $f ($#firstLine_fields vs $#expected_firstLine_fields)" unless($#firstLine_fields == $#expected_firstLine_fields); for(my $i = 0; $i <= $#firstLine_fields; $i++) { - die "Incorrect header for $f - expect $expected_firstLine_fields[$i], got $firstLine_fields[$i]" unless($firstLine_fields[$i] eq $expected_firstLine_fields[$i]); + die "Incorrect header for $f" unless($firstLine_fields[$i] eq $expected_firstLine_fields[$i]); } my $n_contigs = 0; @@ -356,16 +348,9 @@ my $target_extraction = $working_dir_thisSample . '/extraction.bam'; -my $threads_minus_1 = $maxThreads - 1; -die unless($threads_minus_1 >= 0); my $target_extraction_mapped = $working_dir_thisSample . '/extraction_mapped.bam'; -if($samtools_T) -{ - die "File $samtools_T specified via --samtools_T not existing" unless(-e $samtools_T); -} -my $view_T_switch = ($samtools_T) ? " -T $samtools_T " : ""; -my $extraction_command = qq($samtools_bin view -\@ $threads_minus_1 $view_T_switch -bo $target_extraction_mapped $BAM ).join(' ', @refIDs_for_extraction); +my $extraction_command = qq($samtools_bin view -bo $target_extraction_mapped $BAM ).join(' ', @refIDs_for_extraction); print "Extract reads from ", scalar(@refIDs_for_extraction), " regions...\n"; if(system($extraction_command) != 0) { @@ -376,7 +361,7 @@ { my $target_extraction_unmapped = $working_dir_thisSample . '/extraction_unmapped.bam'; - my $extraction_command_unmapped = qq($samtools_bin view -\@ $threads_minus_1 $view_T_switch $BAM '*' | awk '{if (\$3 == "*") print \$0}' | $samtools_bin view -bo $target_extraction_unmapped -); + my $extraction_command_unmapped = qq($samtools_bin view $BAM '*' | awk '{if (\$3 == "*") print \$0}' | $samtools_bin view -bo $target_extraction_unmapped -); print "Extract unmapped reads...\n"; if(system($extraction_command_unmapped) != 0) From fe2c0a19e72733bce944be7f66b5cfc940dc5426 Mon Sep 17 00:00:00 2001 From: jafors Date: Tue, 14 Jan 2020 16:00:31 +0100 Subject: [PATCH 09/33] revert unnecessary changes --- HLA-LA.pl | 25 ++++++++++++++++++++----- 1 file changed, 20 insertions(+), 5 deletions(-) diff --git a/HLA-LA.pl b/HLA-LA.pl index 060a562..b94a032 100755 --- a/HLA-LA.pl +++ b/HLA-LA.pl @@ -29,6 +29,7 @@ my $extractExonkMerCounts; my $longReads = 0; my $testing = 0; +my $samtools_T; GetOptions ( 'BAM:s' => \$_BAM, 'graph:s' => \$graph, @@ -45,6 +46,7 @@ 'extractExonkMerCounts:s' => \$extractExonkMerCounts, 'longReads:s' => \$longReads, 'testing:s' => \$testing, + 'samtools_T:s' => \$samtools_T, ); if ($extractExonkMerCounts) @@ -150,7 +152,6 @@ } my $working_dir_thisSample = $working_dir . '/' . $sampleID; - print "HLA-LA.pl\n\n"; print "Identified paths:\n"; @@ -199,6 +200,7 @@ print "Using custom graph directory $customGraphDir\n"; $full_graph_dir = $customGraphDir . '/' . $graph; } + my $known_references_dir = $full_graph_dir . '/knownReferences'; unless(-e $full_graph_dir) { @@ -209,6 +211,11 @@ die "Graph directory $full_graph_dir does not seem to be complete - does this directory specify a valid graph for HLA-LA?"; } +unless((-e $full_graph_dir . '/serializedGRAPH')) +{ + die "It seems that you have not yet indexed graph $graph - suggested command: ../bin/HLA-LA --action prepareGraph --PRG_graph_dir ../graphs/${graph}"; +} + # get index for this BAM my $command_idxstats = qq($samtools_bin idxstats $BAM); my $command_idxstats_output = `$command_idxstats`; @@ -233,8 +240,9 @@ my $additional_references_dir = $this_bin_dir . '/additionalReferences/' . $graph; if ($customGraphDir and (-e $customGraphDir)) { - $additional_references_dir = $full_graph_dir . '/../additionalReferences/' . $graph; + $additional_references_dir = $full_graph_dir . '/../additionalReferences/' . $graph; } + if(-e $additional_references_dir) { my @additional_files_references = glob($additional_references_dir . '/*.txt'); @@ -263,7 +271,7 @@ die "Incorrect header for $f ($#firstLine_fields vs $#expected_firstLine_fields)" unless($#firstLine_fields == $#expected_firstLine_fields); for(my $i = 0; $i <= $#firstLine_fields; $i++) { - die "Incorrect header for $f" unless($firstLine_fields[$i] eq $expected_firstLine_fields[$i]); + die "Incorrect header for $f - expect $expected_firstLine_fields[$i], got $firstLine_fields[$i]" unless($firstLine_fields[$i] eq $expected_firstLine_fields[$i]); } my $n_contigs = 0; @@ -348,9 +356,16 @@ my $target_extraction = $working_dir_thisSample . '/extraction.bam'; +my $threads_minus_1 = $maxThreads - 1; +die unless($threads_minus_1 >= 0); my $target_extraction_mapped = $working_dir_thisSample . '/extraction_mapped.bam'; -my $extraction_command = qq($samtools_bin view -bo $target_extraction_mapped $BAM ).join(' ', @refIDs_for_extraction); +if($samtools_T) +{ + die "File $samtools_T specified via --samtools_T not existing" unless(-e $samtools_T); +} +my $view_T_switch = ($samtools_T) ? " -T $samtools_T " : ""; +my $extraction_command = qq($samtools_bin view -\@ $threads_minus_1 $view_T_switch -bo $target_extraction_mapped $BAM ).join(' ', @refIDs_for_extraction); print "Extract reads from ", scalar(@refIDs_for_extraction), " regions...\n"; if(system($extraction_command) != 0) { @@ -361,7 +376,7 @@ { my $target_extraction_unmapped = $working_dir_thisSample . '/extraction_unmapped.bam'; - my $extraction_command_unmapped = qq($samtools_bin view $BAM '*' | awk '{if (\$3 == "*") print \$0}' | $samtools_bin view -bo $target_extraction_unmapped -); + my $extraction_command_unmapped = qq($samtools_bin view -\@ $threads_minus_1 $view_T_switch $BAM '*' | awk '{if (\$3 == "*") print \$0}' | $samtools_bin view -bo $target_extraction_unmapped -); print "Extract unmapped reads...\n"; if(system($extraction_command_unmapped) != 0) From d386509406105391732aadf621731144d49c49fa Mon Sep 17 00:00:00 2001 From: jafors Date: Thu, 16 Jan 2020 18:27:18 +0100 Subject: [PATCH 10/33] Removed changes on additionalReferencesDir --- HLA-LA.pl | 4 ---- 1 file changed, 4 deletions(-) diff --git a/HLA-LA.pl b/HLA-LA.pl index b94a032..29c0e80 100755 --- a/HLA-LA.pl +++ b/HLA-LA.pl @@ -238,10 +238,6 @@ my @files_references = glob($known_references_dir . '/*.txt'); die "No known reference files in knownReferences ($full_graph_dir)?" unless(@files_references); my $additional_references_dir = $this_bin_dir . '/additionalReferences/' . $graph; -if ($customGraphDir and (-e $customGraphDir)) -{ - $additional_references_dir = $full_graph_dir . '/../additionalReferences/' . $graph; -} if(-e $additional_references_dir) { From 5311e5b3bf1d3a0031c5bec660bd3225ce225f63 Mon Sep 17 00:00:00 2001 From: Alexander Dilthey Date: Fri, 7 Feb 2020 17:40:40 +0100 Subject: [PATCH 11/33] Report contig strandesness --- HLA-ASM.pl | 23 +++++++++++++---------- 1 file changed, 13 insertions(+), 10 deletions(-) diff --git a/HLA-ASM.pl b/HLA-ASM.pl index 050b3c9..87f6090 100755 --- a/HLA-ASM.pl +++ b/HLA-ASM.pl @@ -210,8 +210,9 @@ BEGIN print DOTPLOTDATA join("\t", "region", "contigID", "refID", "refCoordinate", "contigCoordinate"), "\n"; print EDITDISTANCE join("\t", "region", "contigID", "refID", "editDistance"), "\n"; print CONTIGLENGTHS join("\t", "region", "refID", "length"), "\n"; -print GENEPOSITIONS join("\t", "contigID", "gene", "definedFromRefID", "startInContig_0Based", "stopInContig_0Based", "capturedParts"), "\n"; +print GENEPOSITIONS join("\t", "contigID", "contigStrand", "gene", "definedFromRefID", "startInContig_0Based_relativeToSpecifiedStrand", "stopInContig_0Based_relativeToSpecifiedStrand", "capturedParts"), "\n"; +my %overlappingContig_strand_called; my %results; foreach my $region (sort keys %relevantRegions) { @@ -318,7 +319,6 @@ BEGIN my %overlappingContigs; my %overlappingContigs_idty; my %overlappingContig_strands; - my %overlappingContig_strand_called; my %strand_per_originalContig; my %strand_per_haplotig; @@ -479,7 +479,7 @@ BEGIN # } die unless(defined $strand); - $overlappingContig_strand_called{$contigID} = $strand; + $overlappingContig_strand_called{$region}{$contigID} = $strand; my $contigSequence = $contigs_href->{$contigID}; if(defined $strand and ($strand eq '-')) @@ -944,8 +944,8 @@ BEGIN die unless (defined $found_starts_alignmentCoordinates{$k}); - my $skipped_query_alignment = substr($alignments_per_refContig{$refContigID}[2], 0, $found_starts_alignmentCoordinates{$k}); - $skipped_query_alignment =~ s/-//g; + # my $skipped_query_alignment = substr($alignments_per_refContig{$refContigID}[2], 0, $found_starts_alignmentCoordinates{$k}); + # $skipped_query_alignment =~ s/-//g; # die unless($found_starts_alignmentCoordinates{$k}); # my $total_alignment_till_end_plus_1 = substr($alignments_per_refContig{$refContigID}[2], 0, $found_starts_alignmentCoordinates{$k} + 1); @@ -953,13 +953,15 @@ BEGIN # $extractedSequences_pos{$k} = [length($skipped_query_alignment), length($total_alignment_till_end_plus_1)]; + # note to self: not quite clear what the logic here is - first we set my $skipped_query_alignment = ''; if($found_starts_alignmentCoordinates{$k}) { $skipped_query_alignment = substr($alignments_per_refContig{$refContigID}[2], 0, $found_starts_alignmentCoordinates{$k}); } - $skipped_query_alignment =~ s/-//g; + $skipped_query_alignment =~ s/-//g; + my $first_queryCoordinate = length($skipped_query_alignment); my $last_queryCoordinate = $first_queryCoordinate + length($extracted_contig_alignment_noGap) - 1; if(length($extracted_contig_alignment_noGap) == 0) @@ -1008,8 +1010,8 @@ BEGIN { die unless(defined $components_per_gene{$gene}); print GENEPOSITIONS join("\t", - $refContigID, - $contigID, + $contigID, + $overlappingContig_strand_called{'MHC'}{$contigID}, $gene, $refContigID, min(@positions), @@ -1266,14 +1268,15 @@ BEGIN my $summaryFn = $working_dir . '/' . $sampleID . '/summary.txt'; open(SUMMARY, '>', $summaryFn) or die "Cannot open $summaryFn"; -print SUMMARY join("\t", qw/contigID locus utilizedRefContig start stop calledGenotypes components editDistance_calledGenotypes_assembly minEditDistance_assembly_truth minEditDistance_calledGenotype_truth minEditDistance_assembly_truth_whichAlleles minEditDistance_calledGenotype_truth_whichAlleles/), "\n"; +print SUMMARY join("\t", qw/contigID contigStrand locus utilizedRefContig startInContig_relativeToSpecifiedStrand stopInContig_relativeToSpecifiedStrand calledGenotypes components editDistance_calledGenotypes_assembly minEditDistance_assembly_truth minEditDistance_calledGenotype_truth minEditDistance_assembly_truth_whichAlleles minEditDistance_calledGenotype_truth_whichAlleles/), "\n"; foreach my $locus (sort {$a cmp $b} keys %results_by_locus) { foreach my $contigID (sort {$a cmp $b} keys %{$results_by_locus{$locus}}) { if((not $max_report_edit_distance) or ($results_by_locus{$locus}{$contigID}[5] <= $max_report_edit_distance)) { - print SUMMARY join("\t", $contigID, $locus, @{$results_by_locus{$locus}{$contigID}}), "\n"; + die unless(defined $overlappingContig_strand_called{'MHC'}{$contigID}); + print SUMMARY join("\t", $contigID, $overlappingContig_strand_called{'MHC'}{$contigID}, $locus, @{$results_by_locus{$locus}{$contigID}}), "\n"; } } } From 72d54dce76e5914a149528cbff7e5cf7984c6254 Mon Sep 17 00:00:00 2001 From: Jan Forster <31272349+jafors@users.noreply.github.com> Date: Sun, 23 Aug 2020 20:14:17 +0200 Subject: [PATCH 12/33] Update findPath.pm Fix samtools version (taken from patch) --- findPath.pm | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/findPath.pm b/findPath.pm index 9db1283..ab1b14d 100644 --- a/findPath.pm +++ b/findPath.pm @@ -11,11 +11,11 @@ sub check_samtools die "Can't parse samtools version output" unless($samtools_version =~ /samtools ([\d\.]+)/); $samtools_version = $1; my $samtools_version_numeric = $samtools_version; - if($samtools_version_numeric =~ /^(\d+)\.(\d+)\.(\d+)$/) - { - $samtools_version_numeric = $1 . '.' . $2 . $3; + $samtools_version_numeric =~ /^(\d+)\.(\d+)/; + my $samtools_version_major = $1; + my $samtools_version_minor = $2; } - unless($samtools_version_numeric >= 1.3) + unless($samtools_version_major > 1 or ($samtools_version_major == 1 and $samtools_version_minor >= 3)) { die "I need samtools >=1.3"; } From d9d27a035111989123772f7c7fbe3fb2e317b077 Mon Sep 17 00:00:00 2001 From: Jan Forster <31272349+jafors@users.noreply.github.com> Date: Sun, 23 Aug 2020 20:41:18 +0200 Subject: [PATCH 13/33] Update findPath.pm Deleted unneeded brackets. --- findPath.pm | 1 - 1 file changed, 1 deletion(-) diff --git a/findPath.pm b/findPath.pm index ab1b14d..6a0b1e1 100644 --- a/findPath.pm +++ b/findPath.pm @@ -14,7 +14,6 @@ sub check_samtools $samtools_version_numeric =~ /^(\d+)\.(\d+)/; my $samtools_version_major = $1; my $samtools_version_minor = $2; - } unless($samtools_version_major > 1 or ($samtools_version_major == 1 and $samtools_version_minor >= 3)) { die "I need samtools >=1.3"; From 66eb9ae73c7ebe7eb4198656fb0dda0dab62c810 Mon Sep 17 00:00:00 2001 From: Jan Forster <31272349+jafors@users.noreply.github.com> Date: Mon, 24 Aug 2020 19:44:21 +0200 Subject: [PATCH 14/33] Update HLA-LA.pl Fixed samtools version check --- HLA-LA.pl | 9 ++++----- 1 file changed, 4 insertions(+), 5 deletions(-) diff --git a/HLA-LA.pl b/HLA-LA.pl index 29c0e80..f0caa15 100755 --- a/HLA-LA.pl +++ b/HLA-LA.pl @@ -174,11 +174,10 @@ die "Can't parse samtools version output" unless($samtools_version =~ /samtools ([\d\.]+)/); $samtools_version = $1; my $samtools_version_numeric = $samtools_version; -if($samtools_version_numeric =~ /^(\d+)\.(\d+)\.(\d+)$/) -{ - $samtools_version_numeric = $1 . '.' . $2 . $3; -} -unless($samtools_version_numeric >= 1.3) +$samtools_version_numeric =~ /^(\d+)\.(\d+)/; +my $samtools_version_major = $1; +my $samtools_version_minor = $2; +unless($samtools_version_major > 1 or ($samtools_version_major == 1 and $samtools_version_minor >= 3)) { die "I need samtools >=1.3"; } From b190dbe4f239672e161a05d9a5bc0eb059a8dcbe Mon Sep 17 00:00:00 2001 From: Jan Forster <31272349+jafors@users.noreply.github.com> Date: Tue, 25 Aug 2020 12:54:28 +0200 Subject: [PATCH 15/33] Add prepareGraph to HLA-LA.pl --- HLA-LA.pl | 29 +++++++++++++++++++++++++++++ 1 file changed, 29 insertions(+) diff --git a/HLA-LA.pl b/HLA-LA.pl index f0caa15..b15d4a4 100755 --- a/HLA-LA.pl +++ b/HLA-LA.pl @@ -14,6 +14,7 @@ $| = 1; my $this_bin_dir = $FindBin::RealBin; +my $prepareGraph; my $_BAM; my $graph; my $customGraphDir; @@ -31,6 +32,7 @@ my $testing = 0; my $samtools_T; GetOptions ( + 'prepareGraph:s' => \$prepareGraph, 'BAM:s' => \$_BAM, 'graph:s' => \$graph, 'customGraphDir:s' => \$customGraphDir, @@ -49,6 +51,33 @@ 'samtools_T:s' => \$samtools_T, ); +if ($prepareGraph) +{ + my $full_graph_dir = $FindBin::RealBin . '/../graphs/' . $graph; + if ($customGraphDir and (-e $customGraphDir)) + { + print "Using custom graph directory $customGraphDir\n"; + $full_graph_dir = $customGraphDir . '/' . $graph; + } + + my $MHC_PRG_2_bin = '../bin/HLA-LA'; + + my $previous_dir = getcwd; + chdir($this_bin_dir) or die "Cannot cd into $this_bin_dir"; + + die "Binary $MHC_PRG_2_bin not there!" unless(-e $MHC_PRG_2_bin); + my $command_MHC_PRG = qq($MHC_PRG_2_bin --action prepareGraph --PRG_graph_dir $full_graph_dir); + + print "\nNow executing:\n$command_MHC_PRG\n"; + + if(system($command_MHC_PRG) != 0) + { + die "HLA-LA graph preparation not successful. Command was $command_MHC_PRG\n"; + } + exit 0; +} + + if ($extractExonkMerCounts) { warn "--extractExonkMerCounts 1: This feature is experimental and unlikely to work on your machine"; From a55f40adc65642b77e779e28ae382ff8d0f0e2fa Mon Sep 17 00:00:00 2001 From: jafors Date: Fri, 28 Aug 2020 15:34:04 +0200 Subject: [PATCH 16/33] correct handling of absolute and relative paths for custom graphdir --- HLA-LA.pl | 23 ++++++++++++++++++----- 1 file changed, 18 insertions(+), 5 deletions(-) diff --git a/HLA-LA.pl b/HLA-LA.pl index b15d4a4..404d699 100755 --- a/HLA-LA.pl +++ b/HLA-LA.pl @@ -54,10 +54,16 @@ if ($prepareGraph) { my $full_graph_dir = $FindBin::RealBin . '/../graphs/' . $graph; - if ($customGraphDir and (-e $customGraphDir)) + if($customGraphDir and (-e $customGraphDir)) { + my $dir = getcwd; print "Using custom graph directory $customGraphDir\n"; - $full_graph_dir = $customGraphDir . '/' . $graph; + $full_graph_dir = $customGraphDir . '/' . $graph; + my $is_absolute = File::Spec->file_name_is_absolute( $full_graph_dir ); + unless($is_absolute) + { + $full_graph_dir = $dir . '/' . $customGraphDir . '/' . $graph; + } } my $MHC_PRG_2_bin = '../bin/HLA-LA'; @@ -223,10 +229,17 @@ } my $full_graph_dir = $FindBin::RealBin . '/../graphs/' . $graph; -if ($customGraphDir and (-e $customGraphDir)) +if($customGraphDir and (-e $customGraphDir)) { - print "Using custom graph directory $customGraphDir\n"; - $full_graph_dir = $customGraphDir . '/' . $graph; + my $dir = getcwd; + print "Using custom graph directory $customGraphDir\n"; + $full_graph_dir = $customGraphDir . '/' . $graph; + my $is_absolute = File::Spec->file_name_is_absolute( $full_graph_dir ); + unless($is_absolute) + { + $full_graph_dir = $dir . '/' . $customGraphDir . '/' . $graph; + } + } my $known_references_dir = $full_graph_dir . '/knownReferences'; From 2de61d2176c492436319711118f42d4797d709af Mon Sep 17 00:00:00 2001 From: jafors Date: Wed, 2 Sep 2020 16:47:19 +0200 Subject: [PATCH 17/33] Cleanup --- HLA-LA.pl | 37 ++++++++++++++++++------------------- 1 file changed, 18 insertions(+), 19 deletions(-) diff --git a/HLA-LA.pl b/HLA-LA.pl index 404d699..dc98787 100755 --- a/HLA-LA.pl +++ b/HLA-LA.pl @@ -14,7 +14,6 @@ $| = 1; my $this_bin_dir = $FindBin::RealBin; -my $prepareGraph; my $_BAM; my $graph; my $customGraphDir; @@ -29,10 +28,10 @@ my $moreReferencesDir; my $extractExonkMerCounts; my $longReads = 0; +my $prepareGraph = 0; my $testing = 0; my $samtools_T; GetOptions ( - 'prepareGraph:s' => \$prepareGraph, 'BAM:s' => \$_BAM, 'graph:s' => \$graph, 'customGraphDir:s' => \$customGraphDir, @@ -47,6 +46,7 @@ 'moreReferencesDir:s' => \$moreReferencesDir, 'extractExonkMerCounts:s' => \$extractExonkMerCounts, 'longReads:s' => \$longReads, + 'prepareGraph:s' => \$prepareGraph, 'testing:s' => \$testing, 'samtools_T:s' => \$samtools_T, ); @@ -56,14 +56,14 @@ my $full_graph_dir = $FindBin::RealBin . '/../graphs/' . $graph; if($customGraphDir and (-e $customGraphDir)) { - my $dir = getcwd; + my $dir = getcwd; print "Using custom graph directory $customGraphDir\n"; - $full_graph_dir = $customGraphDir . '/' . $graph; - my $is_absolute = File::Spec->file_name_is_absolute( $full_graph_dir ); - unless($is_absolute) - { - $full_graph_dir = $dir . '/' . $customGraphDir . '/' . $graph; - } + $full_graph_dir = $customGraphDir . '/' . $graph; + my $is_absolute = File::Spec->file_name_is_absolute( $full_graph_dir ); + unless($is_absolute) + { + $full_graph_dir = $dir . '/' . $customGraphDir . '/' . $graph; + } } my $MHC_PRG_2_bin = '../bin/HLA-LA'; @@ -130,7 +130,7 @@ } elsif($picard_sam2fastq_bin =~ /picard\.jar$/) { - $FASTQ_extraction_command_part1 = qq($java_bin -Xmx10g -XX:-UseGCOverheadLimit -jar $picard_sam2fastq_bin SamToFastq); + $FASTQ_extraction_command_part1 = qq($java_bin -Xmx10g -XX:-UseGCOverheadLimit -jar $picard_sam2fastq_bin SamToFastq); } elsif($picard_sam2fastq_bin =~ /picard$/) { @@ -231,15 +231,14 @@ my $full_graph_dir = $FindBin::RealBin . '/../graphs/' . $graph; if($customGraphDir and (-e $customGraphDir)) { - my $dir = getcwd; - print "Using custom graph directory $customGraphDir\n"; - $full_graph_dir = $customGraphDir . '/' . $graph; - my $is_absolute = File::Spec->file_name_is_absolute( $full_graph_dir ); - unless($is_absolute) - { - $full_graph_dir = $dir . '/' . $customGraphDir . '/' . $graph; - } - + my $dir = getcwd; + print "Using custom graph directory $customGraphDir\n"; + $full_graph_dir = $customGraphDir . '/' . $graph; + my $is_absolute = File::Spec->file_name_is_absolute( $full_graph_dir ); + unless($is_absolute) + { + $full_graph_dir = $dir . '/' . $customGraphDir . '/' . $graph; + } } my $known_references_dir = $full_graph_dir . '/knownReferences'; From 2aa3d161ea5d056c0dfcf93cbc1cab51d1a2dc9a Mon Sep 17 00:00:00 2001 From: jafors Date: Wed, 2 Sep 2020 16:50:20 +0200 Subject: [PATCH 18/33] fmt --- HLA-LA.pl | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/HLA-LA.pl b/HLA-LA.pl index dc98787..5a26d38 100755 --- a/HLA-LA.pl +++ b/HLA-LA.pl @@ -130,7 +130,7 @@ } elsif($picard_sam2fastq_bin =~ /picard\.jar$/) { - $FASTQ_extraction_command_part1 = qq($java_bin -Xmx10g -XX:-UseGCOverheadLimit -jar $picard_sam2fastq_bin SamToFastq); + $FASTQ_extraction_command_part1 = qq($java_bin -Xmx10g -XX:-UseGCOverheadLimit -jar $picard_sam2fastq_bin SamToFastq); } elsif($picard_sam2fastq_bin =~ /picard$/) { From f636b62563ed85408ceaf667f6fc93838442b9b2 Mon Sep 17 00:00:00 2001 From: Alexander Dilthey Date: Thu, 1 Oct 2020 21:06:46 +0200 Subject: [PATCH 19/33] Reference added --- .../PRG_MHC_GRCh38_withIMGT/G1000_Ymasked.txt | 3325 +++++++++++++++++ 1 file changed, 3325 insertions(+) create mode 100644 additionalReferences/PRG_MHC_GRCh38_withIMGT/G1000_Ymasked.txt diff --git a/additionalReferences/PRG_MHC_GRCh38_withIMGT/G1000_Ymasked.txt b/additionalReferences/PRG_MHC_GRCh38_withIMGT/G1000_Ymasked.txt new file mode 100644 index 0000000..0d46a51 --- /dev/null +++ b/additionalReferences/PRG_MHC_GRCh38_withIMGT/G1000_Ymasked.txt @@ -0,0 +1,3325 @@ +contigID contigLength ExtractCompleteContig PartialExtraction_Start PartialExtraction_Stop +chr1 248956422 0 +chr2 242193529 0 +chr3 198295559 0 +chr4 190214555 0 +chr5 181538259 0 +chr6 170805979 0 28510120 33480577 +chr7 159345973 0 +chr8 145138636 0 +chr9 138394717 0 +chr10 133797422 0 +chr11 135086622 0 +chr12 133275309 0 +chr13 114364328 0 +chr14 107043718 0 +chr15 101991189 0 +chr16 90338345 0 +chr17 83257441 0 +chr18 80373285 0 +chr19 58617616 0 +chr20 64444167 0 +chr21 46709983 0 +chr22 50818468 0 +chrX 156040895 0 +chrY 57227415 0 +chrUn_KI270302v1 2274 0 +chrUn_KI270304v1 2165 0 +chrUn_KI270303v1 1942 0 +chrUn_KI270305v1 1472 0 +chrUn_KI270322v1 21476 0 +chrUn_KI270320v1 4416 0 +chrUn_KI270310v1 1201 0 +chrUn_KI270316v1 1444 0 +chrUn_KI270315v1 2276 0 +chrUn_KI270312v1 998 0 +chrUn_KI270311v1 12399 0 +chrUn_KI270317v1 37690 0 +chrUn_KI270412v1 1179 0 +chrUn_KI270411v1 2646 0 +chrUn_KI270414v1 2489 0 +chrUn_KI270419v1 1029 0 +chrUn_KI270418v1 2145 0 +chrUn_KI270420v1 2321 0 +chrUn_KI270424v1 2140 0 +chrUn_KI270417v1 2043 0 +chrUn_KI270422v1 1445 0 +chrUn_KI270423v1 981 0 +chrUn_KI270425v1 1884 0 +chrUn_KI270429v1 1361 0 +chrUn_KI270442v1 392061 0 +chrUn_KI270466v1 1233 0 +chrUn_KI270465v1 1774 0 +chrUn_KI270467v1 3920 0 +chrUn_KI270435v1 92983 0 +chrUn_KI270438v1 112505 0 +chrUn_KI270468v1 4055 0 +chrUn_KI270510v1 2415 0 +chrUn_KI270509v1 2318 0 +chrUn_KI270518v1 2186 0 +chrUn_KI270508v1 1951 0 +chrUn_KI270516v1 1300 0 +chrUn_KI270512v1 22689 0 +chrUn_KI270519v1 138126 0 +chrUn_KI270522v1 5674 0 +chrUn_KI270511v1 8127 0 +chrUn_KI270515v1 6361 0 +chrUn_KI270507v1 5353 0 +chrUn_KI270517v1 3253 0 +chrUn_KI270529v1 1899 0 +chrUn_KI270528v1 2983 0 +chrUn_KI270530v1 2168 0 +chrUn_KI270539v1 993 0 +chrUn_KI270538v1 91309 0 +chrUn_KI270544v1 1202 0 +chrUn_KI270548v1 1599 0 +chrUn_KI270583v1 1400 0 +chrUn_KI270587v1 2969 0 +chrUn_KI270580v1 1553 0 +chrUn_KI270581v1 7046 0 +chrUn_KI270579v1 31033 0 +chrUn_KI270589v1 44474 0 +chrUn_KI270590v1 4685 0 +chrUn_KI270584v1 4513 0 +chrUn_KI270582v1 6504 0 +chrUn_KI270588v1 6158 0 +chrUn_KI270593v1 3041 0 +chrUn_KI270591v1 5796 0 +chrUn_KI270330v1 1652 0 +chrUn_KI270329v1 1040 0 +chrUn_KI270334v1 1368 0 +chrUn_KI270333v1 2699 0 +chrUn_KI270335v1 1048 0 +chrUn_KI270338v1 1428 0 +chrUn_KI270340v1 1428 0 +chrUn_KI270336v1 1026 0 +chrUn_KI270337v1 1121 0 +chrUn_KI270363v1 1803 0 +chrUn_KI270364v1 2855 0 +chrUn_KI270362v1 3530 0 +chrUn_KI270366v1 8320 0 +chrUn_KI270378v1 1048 0 +chrUn_KI270379v1 1045 0 +chrUn_KI270389v1 1298 0 +chrUn_KI270390v1 2387 0 +chrUn_KI270387v1 1537 0 +chrUn_KI270395v1 1143 0 +chrUn_KI270396v1 1880 0 +chrUn_KI270388v1 1216 0 +chrUn_KI270394v1 970 0 +chrUn_KI270386v1 1788 0 +chrUn_KI270391v1 1484 0 +chrUn_KI270383v1 1750 0 +chrUn_KI270393v1 1308 0 +chrUn_KI270384v1 1658 0 +chrUn_KI270392v1 971 0 +chrUn_KI270381v1 1930 0 +chrUn_KI270385v1 990 0 +chrUn_KI270382v1 4215 0 +chrUn_KI270376v1 1136 0 +chrUn_KI270374v1 2656 0 +chrUn_KI270372v1 1650 0 +chrUn_KI270373v1 1451 0 +chrUn_KI270375v1 2378 0 +chrUn_KI270371v1 2805 0 +chrUn_KI270448v1 7992 0 +chrUn_KI270521v1 7642 0 +chrUn_GL000195v1 182896 0 +chrUn_GL000219v1 179198 0 +chrUn_GL000220v1 161802 0 +chrUn_GL000224v1 179693 0 +chrUn_KI270741v1 157432 0 +chrUn_GL000226v1 15008 0 +chrUn_GL000213v1 164239 0 +chrUn_KI270743v1 210658 0 +chrUn_KI270744v1 168472 0 +chrUn_KI270745v1 41891 0 +chrUn_KI270746v1 66486 0 +chrUn_KI270747v1 198735 0 +chrUn_KI270748v1 93321 0 +chrUn_KI270749v1 158759 0 +chrUn_KI270750v1 148850 0 +chrUn_KI270751v1 150742 0 +chrUn_KI270752v1 27745 0 +chrUn_KI270753v1 62944 0 +chrUn_KI270754v1 40191 0 +chrUn_KI270755v1 36723 0 +chrUn_KI270756v1 79590 0 +chrUn_KI270757v1 71251 0 +chrUn_GL000214v1 137718 0 +chrUn_KI270742v1 186739 0 +chrUn_GL000216v2 176608 0 +chrUn_GL000218v1 161147 0 +chr1_KI270762v1_alt 354444 0 +chr1_KI270766v1_alt 256271 0 +chr1_KI270760v1_alt 109528 0 +chr1_KI270765v1_alt 185285 0 +chr1_GL383518v1_alt 182439 0 +chr1_GL383519v1_alt 110268 0 +chr1_GL383520v2_alt 366580 0 +chr1_KI270764v1_alt 50258 0 +chr1_KI270763v1_alt 911658 0 +chr1_KI270759v1_alt 425601 0 +chr1_KI270761v1_alt 165834 0 +chr2_KI270770v1_alt 136240 0 +chr2_KI270773v1_alt 70887 0 +chr2_KI270774v1_alt 223625 0 +chr2_KI270769v1_alt 120616 0 +chr2_GL383521v1_alt 143390 0 +chr2_KI270772v1_alt 133041 0 +chr2_KI270775v1_alt 138019 0 +chr2_KI270771v1_alt 110395 0 +chr2_KI270768v1_alt 110099 0 +chr2_GL582966v2_alt 96131 0 +chr2_GL383522v1_alt 123821 0 +chr2_KI270776v1_alt 174166 0 +chr2_KI270767v1_alt 161578 0 +chr3_JH636055v2_alt 173151 0 +chr3_KI270783v1_alt 109187 0 +chr3_KI270780v1_alt 224108 0 +chr3_GL383526v1_alt 180671 0 +chr3_KI270777v1_alt 173649 0 +chr3_KI270778v1_alt 248252 0 +chr3_KI270781v1_alt 113034 0 +chr3_KI270779v1_alt 205312 0 +chr3_KI270782v1_alt 162429 0 +chr3_KI270784v1_alt 184404 0 +chr4_KI270790v1_alt 220246 0 +chr4_GL383528v1_alt 376187 0 +chr4_KI270787v1_alt 111943 0 +chr4_GL000257v2_alt 586476 0 +chr4_KI270788v1_alt 158965 0 +chr4_GL383527v1_alt 164536 0 +chr4_KI270785v1_alt 119912 0 +chr4_KI270789v1_alt 205944 0 +chr4_KI270786v1_alt 244096 0 +chr5_KI270793v1_alt 126136 0 +chr5_KI270792v1_alt 179043 0 +chr5_KI270791v1_alt 195710 0 +chr5_GL383532v1_alt 82728 0 +chr5_GL949742v1_alt 226852 0 +chr5_KI270794v1_alt 164558 0 +chr5_GL339449v2_alt 1612928 0 +chr5_GL383530v1_alt 101241 0 +chr5_KI270796v1_alt 172708 0 +chr5_GL383531v1_alt 173459 0 +chr5_KI270795v1_alt 131892 0 +chr6_GL000250v2_alt 4672374 1 +chr6_KI270800v1_alt 175808 0 +chr6_KI270799v1_alt 152148 0 +chr6_GL383533v1_alt 124736 0 +chr6_KI270801v1_alt 870480 0 +chr6_KI270802v1_alt 75005 0 +chr6_KB021644v2_alt 185823 0 +chr6_KI270797v1_alt 197536 0 +chr6_KI270798v1_alt 271782 0 +chr7_KI270804v1_alt 157952 0 +chr7_KI270809v1_alt 209586 0 +chr7_KI270806v1_alt 158166 0 +chr7_GL383534v2_alt 119183 0 +chr7_KI270803v1_alt 1111570 0 +chr7_KI270808v1_alt 271455 0 +chr7_KI270807v1_alt 126434 0 +chr7_KI270805v1_alt 209988 0 +chr8_KI270818v1_alt 145606 0 +chr8_KI270812v1_alt 282736 0 +chr8_KI270811v1_alt 292436 0 +chr8_KI270821v1_alt 985506 0 +chr8_KI270813v1_alt 300230 0 +chr8_KI270822v1_alt 624492 0 +chr8_KI270814v1_alt 141812 0 +chr8_KI270810v1_alt 374415 0 +chr8_KI270819v1_alt 133535 0 +chr8_KI270820v1_alt 36640 0 +chr8_KI270817v1_alt 158983 0 +chr8_KI270816v1_alt 305841 0 +chr8_KI270815v1_alt 132244 0 +chr9_GL383539v1_alt 162988 0 +chr9_GL383540v1_alt 71551 0 +chr9_GL383541v1_alt 171286 0 +chr9_GL383542v1_alt 60032 0 +chr9_KI270823v1_alt 439082 0 +chr10_GL383545v1_alt 179254 0 +chr10_KI270824v1_alt 181496 0 +chr10_GL383546v1_alt 309802 0 +chr10_KI270825v1_alt 188315 0 +chr11_KI270832v1_alt 210133 0 +chr11_KI270830v1_alt 177092 0 +chr11_KI270831v1_alt 296895 0 +chr11_KI270829v1_alt 204059 0 +chr11_GL383547v1_alt 154407 0 +chr11_JH159136v1_alt 200998 0 +chr11_JH159137v1_alt 191409 0 +chr11_KI270827v1_alt 67707 0 +chr11_KI270826v1_alt 186169 0 +chr12_GL877875v1_alt 167313 0 +chr12_GL877876v1_alt 408271 0 +chr12_KI270837v1_alt 40090 0 +chr12_GL383549v1_alt 120804 0 +chr12_KI270835v1_alt 238139 0 +chr12_GL383550v2_alt 169178 0 +chr12_GL383552v1_alt 138655 0 +chr12_GL383553v2_alt 152874 0 +chr12_KI270834v1_alt 119498 0 +chr12_GL383551v1_alt 184319 0 +chr12_KI270833v1_alt 76061 0 +chr12_KI270836v1_alt 56134 0 +chr13_KI270840v1_alt 191684 0 +chr13_KI270839v1_alt 180306 0 +chr13_KI270843v1_alt 103832 0 +chr13_KI270841v1_alt 169134 0 +chr13_KI270838v1_alt 306913 0 +chr13_KI270842v1_alt 37287 0 +chr14_KI270844v1_alt 322166 0 +chr14_KI270847v1_alt 1511111 0 +chr14_KI270845v1_alt 180703 0 +chr14_KI270846v1_alt 1351393 0 +chr15_KI270852v1_alt 478999 0 +chr15_KI270851v1_alt 263054 0 +chr15_KI270848v1_alt 327382 0 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1945 0 +chrUn_KN707632v1_decoy 1424 0 +chrUn_KN707633v1_decoy 1274 0 +chrUn_KN707634v1_decoy 1007 0 +chrUn_KN707635v1_decoy 1414 0 +chrUn_KN707636v1_decoy 1725 0 +chrUn_KN707637v1_decoy 5354 0 +chrUn_KN707638v1_decoy 2189 0 +chrUn_KN707639v1_decoy 1294 0 +chrUn_KN707640v1_decoy 1831 0 +chrUn_KN707641v1_decoy 1647 0 +chrUn_KN707642v1_decoy 2943 0 +chrUn_KN707643v1_decoy 2857 0 +chrUn_KN707644v1_decoy 1030 0 +chrUn_KN707645v1_decoy 1070 0 +chrUn_KN707646v1_decoy 1735 0 +chrUn_KN707647v1_decoy 1982 0 +chrUn_KN707648v1_decoy 1564 0 +chrUn_KN707649v1_decoy 1775 0 +chrUn_KN707650v1_decoy 1540 0 +chrUn_KN707651v1_decoy 2013 0 +chrUn_KN707652v1_decoy 1176 0 +chrUn_KN707653v1_decoy 1890 0 +chrUn_KN707654v1_decoy 3644 0 +chrUn_KN707655v1_decoy 2785 0 +chrUn_KN707656v1_decoy 1017 0 +chrUn_KN707657v1_decoy 1068 0 +chrUn_KN707658v1_decoy 1007 0 +chrUn_KN707659v1_decoy 2605 0 +chrUn_KN707660v1_decoy 8410 0 +chrUn_KN707661v1_decoy 5534 0 +chrUn_KN707662v1_decoy 2173 0 +chrUn_KN707663v1_decoy 1065 0 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changed, 457 insertions(+) create mode 100644 additionalReferences/PRG_MHC_GRCh38_withIMGT/Additional_B38_2.txt diff --git a/additionalReferences/PRG_MHC_GRCh38_withIMGT/Additional_B38_2.txt b/additionalReferences/PRG_MHC_GRCh38_withIMGT/Additional_B38_2.txt new file mode 100644 index 0000000..c79d3bd --- /dev/null +++ b/additionalReferences/PRG_MHC_GRCh38_withIMGT/Additional_B38_2.txt @@ -0,0 +1,457 @@ +contigID contigLength ExtractCompleteContig PartialExtraction_Start PartialExtraction_Stop +NC_000001.11 248956422 0 +NT_187361.1 175055 0 +NT_187362.1 32032 0 +NT_187363.1 127682 0 +NT_187364.1 66860 0 +NT_187365.1 40176 0 +NT_187366.1 42210 0 +NT_187367.1 176043 0 +NT_187368.1 40745 0 +NT_187369.1 41717 0 +NC_000002.12 242193529 0 +NT_187370.1 161471 0 +NT_187371.1 153799 0 +NC_000003.12 198295559 0 +NT_167215.1 155397 0 +NC_000004.12 190214555 0 +NT_113793.3 209709 0 +NC_000005.10 181538259 0 +NT_113948.1 92689 0 +NC_000006.12 170805979 0 28510120 33480577 +NC_000007.14 159345973 0 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+NT_187656.1 106711 +NT_187657.1 214625 +NT_187658.1 572349 +NT_187659.1 196384 +NT_187660.1 5161414 +NT_187662.1 137721 +NT_187664.1 157099 +NT_187661.1 325800 +NW_003871093.1 88070 +NT_187663.1 1423190 +NT_187665.1 174061 +NT_187666.1 157710 +NW_003571055.2 729520 +NW_004504305.1 74013 +NT_187667.1 274009 +NT_187668.1 205194 +NT_187669.1 170665 +NT_187670.1 184516 +NT_187671.1 190932 +NT_187672.1 123111 +NT_187673.1 170701 +NT_187674.1 198005 +NT_187675.1 282224 +NT_187676.1 187935 +NT_187677.1 189352 +NT_187678.1 166540 +NT_187679.1 555799 +NT_167245.2 4604811 1 +NT_187680.1 229282 +NT_187681.1 218612 +NW_003571056.2 1064304 +NT_187682.1 176103 +NT_187683.1 186203 +NT_187684.1 200773 +NT_187685.1 170148 +NT_187686.1 215732 +NT_187687.1 170537 +NT_113949.2 177381 +NT_187688.1 163458 +NT_167246.2 4677643 1 +NW_003571057.2 1091841 +NT_187689.1 197351 +NT_167247.2 4827813 1 +NW_003571058.2 1066390 +NT_187690.1 164170 +NT_167248.2 4606388 1 +NW_003571059.2 1002683 +NT_187691.1 165607 +NT_167249.2 4929269 1 +NW_003571060.1 987100 +NT_187692.1 76752 1 +NW_003571061.2 796479 +NT_187693.1 1066800 +NC_012920.1 16569 +* 0 0 From a41f3ed6c1eac79d6827dcf716a8069e3c516797 Mon Sep 17 00:00:00 2001 From: irunonayran Date: Wed, 22 Jun 2022 16:36:06 +0200 Subject: [PATCH 21/33] remove unnecessary db:HTS module --- HLA-ASM.pl | 1 - 1 file changed, 1 deletion(-) diff --git a/HLA-ASM.pl b/HLA-ASM.pl index 87f6090..2f648fc 100755 --- a/HLA-ASM.pl +++ b/HLA-ASM.pl @@ -26,7 +26,6 @@ BEGIN use Getopt::Long; use Cwd qw/getcwd abs_path/; use findPath; -use Bio::DB::HTS; my $scriptPath = $FindBin::Bin; my $includes=" -I" . join(" -I", @INC); From d2a9bd09050b4cb495aeafe1ab65d939886032b9 Mon Sep 17 00:00:00 2001 From: Alexander Dilthey Date: Mon, 17 Jul 2023 10:56:13 +0200 Subject: [PATCH 22/33] Allow for dashes in sample names --- HLA-LA.pl | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/HLA-LA.pl b/HLA-LA.pl index 5a26d38..fa9363a 100755 --- a/HLA-LA.pl +++ b/HLA-LA.pl @@ -181,9 +181,9 @@ $working_dir = abs_path($working_dir); -unless($sampleID =~ /^\w+$/) +unless($sampleID =~ /^[\w+\-]$/) { - die "Please use only alphanumeric characters - \\w+ - for --sampleID"; +die "Please use only alphanumeric characters - [\\w+\\-} - for --sampleID"; } my $working_dir_thisSample = $working_dir . '/' . $sampleID; From ac6fdfbdc82fafdb711a201464cc1051dce45e60 Mon Sep 17 00:00:00 2001 From: Alexander Dilthey Date: Mon, 17 Jul 2023 11:05:16 +0200 Subject: [PATCH 23/33] Add lib64 library dir for bamtools --- makefile | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/makefile b/makefile index 96e7d8a..19e7745 100644 --- a/makefile +++ b/makefile @@ -9,9 +9,10 @@ BOOST_LIB = $(BOOST_PATH)/lib BAMTOOLS_INCLUDE = $(BAMTOOLS_PATH)/include/bamtools BAMTOOLS_SRC = $(BAMTOOLS_PATH)/src BAMTOOLS_LIB = $(BAMTOOLS_PATH)/lib64 +BAMTOOLS_LIB_2 = $(BAMTOOLS_PATH)/lib INCS = -I$(BOOST_INCLUDE) -I$(BAMTOOLS_INCLUDE) -I$(BAMTOOLS_SRC) -LIBS = -L$(BOOST_LIB) -L$(BAMTOOLS_LIB) -lboost_random -lboost_filesystem -lboost_system -lbamtools -lz -lboost_serialization +LIBS = -L$(BOOST_LIB) -L$(BAMTOOLS_LIB) -L$(BAMTOOLS_LIB_2) -lboost_random -lboost_filesystem -lboost_system -lbamtools -lz -lboost_serialization # use the following for older versions of BamTools (e.g. commit https://github.com/pezmaster31/bamtools/commit/2d7685d2aeedd11c46ad3bd67886d9ed65c30f3e) # ... in which case you probably also have to comment in the '#include "utils/bamtools_utilities.h"' include statement in mapper/processBAM.cpp. From cdd2423e3dd0c87144366f4d13a645ede0afce98 Mon Sep 17 00:00:00 2001 From: Alexander Dilthey Date: Mon, 17 Jul 2023 11:39:42 +0200 Subject: [PATCH 24/33] Bugfix --- HLA-LA.pl | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/HLA-LA.pl b/HLA-LA.pl index fa9363a..2481af5 100755 --- a/HLA-LA.pl +++ b/HLA-LA.pl @@ -181,9 +181,9 @@ $working_dir = abs_path($working_dir); -unless($sampleID =~ /^[\w+\-]$/) +unless($sampleID =~ /^[\w\-]+$/) { -die "Please use only alphanumeric characters - [\\w+\\-} - for --sampleID"; +die "Please use only alphanumeric characters - [\\w\\-]+ - for --sampleID"; } my $working_dir_thisSample = $working_dir . '/' . $sampleID; From 81714dcc4d437e103a24c2143b6653e543d71a9e Mon Sep 17 00:00:00 2001 From: Alexander Dilthey Date: Wed, 19 Jul 2023 14:18:10 +0200 Subject: [PATCH 25/33] Added reference file --- .../Additional_B38_3.txt | 708 ++++++++++++++++++ 1 file changed, 708 insertions(+) create mode 100644 additionalReferences/PRG_MHC_GRCh38_withIMGT/Additional_B38_3.txt diff --git a/additionalReferences/PRG_MHC_GRCh38_withIMGT/Additional_B38_3.txt b/additionalReferences/PRG_MHC_GRCh38_withIMGT/Additional_B38_3.txt new file mode 100644 index 0000000..1fcfa0c --- /dev/null +++ b/additionalReferences/PRG_MHC_GRCh38_withIMGT/Additional_B38_3.txt @@ -0,0 +1,708 @@ +contigID contigLength ExtractCompleteContig PartialExtraction_Start PartialExtraction_Stop +NC_000001.11 248956422 0 +NT_187361.1 175055 0 +NT_187362.1 32032 0 +NT_187363.1 127682 0 +NT_187364.1 66860 0 +NT_187365.1 40176 0 +NT_187366.1 42210 0 +NT_187367.1 176043 0 +NT_187368.1 40745 0 +NT_187369.1 41717 0 +NC_000002.12 242193529 0 +NT_187370.1 161471 0 +NT_187371.1 153799 0 +NC_000003.12 198295559 0 +NT_167215.1 155397 0 +NC_000004.12 190214555 0 +NT_113793.3 209709 0 +NC_000005.10 181538259 0 +NT_113948.1 92689 0 +NC_000006.12 170805979 0 28510120 33480577 +NC_000007.14 159345973 0 +NC_000008.11 145138636 0 +NC_000009.12 138394717 0 +NT_187372.1 40062 0 +NT_187373.1 38054 0 +NT_187374.1 176845 0 +NT_187375.1 39050 0 +NC_000010.11 133797422 0 +NC_000011.10 135086622 0 +NC_000012.12 133275309 0 +NC_000013.11 114364328 0 +NC_000014.9 107043718 0 +NT_113796.3 201709 0 +NT_167219.1 211173 0 +NT_187377.1 194050 0 +NT_113888.1 191469 0 +NT_187378.1 38115 0 +NT_187379.1 39555 0 +NT_187380.1 172810 0 +NT_187381.1 43739 0 +NC_000015.10 101991189 0 +NT_187382.1 448248 0 +NC_000016.10 90338345 0 +NT_187383.1 1872759 0 +NC_000017.11 83257441 0 +NT_113930.2 185591 0 +NT_187384.1 280839 0 +NT_187385.1 112551 0 +NC_000018.10 80373285 0 +NC_000019.10 58617616 0 +NC_000020.11 64444167 0 +NC_000021.9 46709983 0 +NC_000022.11 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+NT_187683.1 186203 0 +NT_187684.1 200773 0 +NT_187685.1 170148 0 +NT_187686.1 215732 0 +NT_187687.1 170537 0 +NT_113949.2 177381 0 +NC_012920.1 16569 0 +* 0 0 + \ No newline at end of file From c123dd506f6af4ac86f2e8004c269d47a155774b Mon Sep 17 00:00:00 2001 From: Alexander Dilthey Date: Wed, 19 Jul 2023 14:43:57 +0200 Subject: [PATCH 26/33] Also allow _ in sample names --- HLA-LA.pl | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/HLA-LA.pl b/HLA-LA.pl index 2481af5..cd3e315 100755 --- a/HLA-LA.pl +++ b/HLA-LA.pl @@ -181,9 +181,9 @@ $working_dir = abs_path($working_dir); -unless($sampleID =~ /^[\w\-]+$/) +unless($sampleID =~ /^[\w\-_]+$/) { -die "Please use only alphanumeric characters - [\\w\\-]+ - for --sampleID"; +die "Please use only alphanumeric characters - [\\w\\-_]+ - for --sampleID"; } my $working_dir_thisSample = $working_dir . '/' . $sampleID; From 00e7663f1ac88f5026d5eb26bd2e2d0d3f37ab89 Mon Sep 17 00:00:00 2001 From: Alexander Dilthey Date: Wed, 19 Jul 2023 15:03:06 +0200 Subject: [PATCH 27/33] Added T2T reference --- .../PRG_MHC_GRCh38_withIMGT/chm13v2.txt | 27 +++++++++++++++++++ 1 file changed, 27 insertions(+) create mode 100644 additionalReferences/PRG_MHC_GRCh38_withIMGT/chm13v2.txt diff --git a/additionalReferences/PRG_MHC_GRCh38_withIMGT/chm13v2.txt b/additionalReferences/PRG_MHC_GRCh38_withIMGT/chm13v2.txt new file mode 100644 index 0000000..d1d723b --- /dev/null +++ b/additionalReferences/PRG_MHC_GRCh38_withIMGT/chm13v2.txt @@ -0,0 +1,27 @@ +contigID contigLength ExtractCompleteContig PartialExtraction_Start PartialExtraction_Stop +chr1 248387328 0 +chr2 242696752 0 +chr3 201105948 0 +chr4 193574945 0 +chr5 182045439 0 +chr6 172126628 28381554 33301857 +chr7 160567428 0 +chr8 146259331 0 +chr9 150617247 0 +chr10 134758134 0 +chr11 135127769 0 +chr12 133324548 0 +chr13 113566686 0 +chr14 101161492 0 +chr15 99753195 0 +chr16 96330374 0 +chr17 84276897 0 +chr18 80542538 0 +chr19 61707364 0 +chr20 66210255 0 +chr21 45090682 0 +chr22 51324926 0 +chrX 154259566 0 +chrY 62460029 0 +chrM 16569 0 +* 0 1 From 92187e8a1a33089d2acc3595e2220e271eb8ac06 Mon Sep 17 00:00:00 2001 From: Alexander Dilthey Date: Wed, 19 Jul 2023 15:04:18 +0200 Subject: [PATCH 28/33] Update README.md --- README.md | 1 + 1 file changed, 1 insertion(+) diff --git a/README.md b/README.md index 5449713..184c69f 100644 --- a/README.md +++ b/README.md @@ -1,6 +1,7 @@ # HLA\*LA (formerly HLA\*PRG:LA) ## News +(19 July 2023) The T2T reference genome (`chm13v2.0.fa`) has now been added to the list of supported references. (10 June 2019) If you work with CRAM files and receive error messages like `Unable to fetch reference #5 28687068..28707018`, the reason is that `samtools view` needs to know which reference genome was used to create your CRAM file. Solution: use the switch `--samtools_T` to specify a suitable reference genome file. Example: `./HLA-LA.pl --BAM NA12878.alt_bwamem_GRCh38DH.20150706.CEU.illumina_platinum_ped.cram --graph PRG_MHC_GRCh38_withIMGT --sampleID NA12878 --samtools_T /path/to/GRCh38_full_analysis_set_plus_decoy_hla.fa`. You need a fresh pull from GitHub for this to work, the bioconda version has not been updated yet. From 624f6fd4c242313018760ee3a1ca5d01e4758b9e Mon Sep 17 00:00:00 2001 From: Alexander Dilthey Date: Thu, 20 Jul 2023 16:22:17 +0200 Subject: [PATCH 29/33] Do not fail if there are no unmapped reads --- HLA-LA.pl | 22 +++++++++++++++++++++- 1 file changed, 21 insertions(+), 1 deletion(-) diff --git a/HLA-LA.pl b/HLA-LA.pl index cd3e315..13fe417 100755 --- a/HLA-LA.pl +++ b/HLA-LA.pl @@ -413,11 +413,31 @@ my $target_extraction_unmapped = $working_dir_thisSample . '/extraction_unmapped.bam'; my $extraction_command_unmapped = qq($samtools_bin view -\@ $threads_minus_1 $view_T_switch $BAM '*' | awk '{if (\$3 == "*") print \$0}' | $samtools_bin view -bo $target_extraction_unmapped -); + print "Extract unmapped reads...\n"; if(system($extraction_command_unmapped) != 0) { - die "Extraction command $extraction_command_unmapped failed"; + + my $count_unmapped = qq($samtools_bin view -\@ $threads_minus_1 $view_T_switch $BAM '*' | awk '{if (\$3 == "*") print \$0}' | wc); + open(COUNT, "$count_unmapped |") or die "Cannot open pipe to count unmapped reads"; + my $wc_out = ; + chomp($wc_out); + close(COUNT); + die "Cannot parse wc output: '$wc_out'" unless($wc_out =~ /^\s*(\d+)\s+(\d+)\s+/); + my $n_unmapped_reads = $1; + + if($n_unmapped_reads != 0) + { + die "Extraction command $extraction_command_unmapped failed - there are unmapped reads [$n_unmapped_reads]"; + } + else + { + print "No unmapped reads, you can ignore the samtools warning if one was emitted...\n"; + my $extraction_command_unmapped_generateEmptyBAM = qq($samtools_bin view -bo $target_extraction_unmapped -\@ $threads_minus_1 $view_T_switch $BAM '*'); + system($extraction_command_unmapped_generateEmptyBAM) and die "Command $extraction_command_unmapped_generateEmptyBAM failed (empty BAM generation, no unmapped reads"; + } + } unlink($target_extraction) if (-e $target_extraction); From c532e1e4805f6a1b5d0496449329b08dc6611f97 Mon Sep 17 00:00:00 2001 From: Alexander Dilthey Date: Thu, 20 Jul 2023 16:22:40 +0200 Subject: [PATCH 30/33] . --- paths.ini | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/paths.ini b/paths.ini index 697acc3..98453e8 100755 --- a/paths.ini +++ b/paths.ini @@ -1,4 +1,4 @@ -picard_sam2fastq_bin=/data/projects/phillippy/software/picard-tools-1.119/SamToFastq.jar,/home/dilthey/picard/picard-tools-1.83/SamToFastq.jar +picard_sam2fastq_bin=/home/dilthey/picard/picard.jar samtools_bin= bwa_bin= nucmer_bin= From 595fb60aecf586eca04ca69ce940d132d405fffa Mon Sep 17 00:00:00 2001 From: Alexander Dilthey Date: Tue, 10 Oct 2023 09:15:04 +0200 Subject: [PATCH 31/33] Create chm13_3.txt --- .../PRG_MHC_GRCh38_withIMGT/chm13_3.txt | 25 +++++++++++++++++++ 1 file changed, 25 insertions(+) create mode 100644 additionalReferences/PRG_MHC_GRCh38_withIMGT/chm13_3.txt diff --git a/additionalReferences/PRG_MHC_GRCh38_withIMGT/chm13_3.txt b/additionalReferences/PRG_MHC_GRCh38_withIMGT/chm13_3.txt new file mode 100644 index 0000000..037c6ca --- /dev/null +++ b/additionalReferences/PRG_MHC_GRCh38_withIMGT/chm13_3.txt @@ -0,0 +1,25 @@ +NC_060925.1 248387328 8 0 +NC_060926.1 242696752 9 0 +NC_060927.1 201105948 9 0 +NC_060928.1 193574945 4 0 +NC_060929.1 182045439 5 0 +NC_060930.1 172126628 28811 0 +NC_060931.1 160567428 1 0 +NC_060932.1 146259331 3 0 +NC_060933.1 150617247 9 0 +NC_060934.1 134758134 1 0 +NC_060935.1 135127769 13 0 +NC_060936.1 133324548 5 0 +NC_060937.1 113566686 2 0 +NC_060938.1 101161492 2 0 +NC_060939.1 99753195 7 0 +NC_060940.1 96330374 14 0 +NC_060941.1 84276897 8 0 +NC_060942.1 80542538 1 0 +NC_060943.1 61707364 4 0 +NC_060944.1 66210255 7 0 +NC_060945.1 45090682 2 0 +NC_060946.1 51324926 15 0 +NC_060947.1 154259566 2 0 +NC_060948.1 62460029 0 0 +* 0 0 2 From be9e7473769f03e4e0d9daf2a8572f094c7ed380 Mon Sep 17 00:00:00 2001 From: Alexander Dilthey Date: Tue, 10 Oct 2023 09:23:23 +0200 Subject: [PATCH 32/33] Update chm13_3.txt --- .../PRG_MHC_GRCh38_withIMGT/chm13_3.txt | 51 ++++++++++--------- 1 file changed, 26 insertions(+), 25 deletions(-) diff --git a/additionalReferences/PRG_MHC_GRCh38_withIMGT/chm13_3.txt b/additionalReferences/PRG_MHC_GRCh38_withIMGT/chm13_3.txt index 037c6ca..29c0804 100644 --- a/additionalReferences/PRG_MHC_GRCh38_withIMGT/chm13_3.txt +++ b/additionalReferences/PRG_MHC_GRCh38_withIMGT/chm13_3.txt @@ -1,25 +1,26 @@ -NC_060925.1 248387328 8 0 -NC_060926.1 242696752 9 0 -NC_060927.1 201105948 9 0 -NC_060928.1 193574945 4 0 -NC_060929.1 182045439 5 0 -NC_060930.1 172126628 28811 0 -NC_060931.1 160567428 1 0 -NC_060932.1 146259331 3 0 -NC_060933.1 150617247 9 0 -NC_060934.1 134758134 1 0 -NC_060935.1 135127769 13 0 -NC_060936.1 133324548 5 0 -NC_060937.1 113566686 2 0 -NC_060938.1 101161492 2 0 -NC_060939.1 99753195 7 0 -NC_060940.1 96330374 14 0 -NC_060941.1 84276897 8 0 -NC_060942.1 80542538 1 0 -NC_060943.1 61707364 4 0 -NC_060944.1 66210255 7 0 -NC_060945.1 45090682 2 0 -NC_060946.1 51324926 15 0 -NC_060947.1 154259566 2 0 -NC_060948.1 62460029 0 0 -* 0 0 2 +contigID contigLength ExtractCompleteContig PartialExtraction_Start PartialExtraction_Stop +NC_060925.1 248387328 0 +NC_060926.1 242696752 0 +NC_060927.1 201105948 0 +NC_060928.1 193574945 0 +NC_060929.1 182045439 0 +NC_060930.1 172126628 28381554 33301857 +NC_060931.1 160567428 0 +NC_060932.1 146259331 0 +NC_060933.1 150617247 0 +NC_060934.1 134758134 0 +NC_060935.1 135127769 0 +NC_060936.1 133324548 0 +NC_060937.1 113566686 0 +NC_060938.1 101161492 0 +NC_060939.1 99753195 0 +NC_060940.1 96330374 0 +NC_060941.1 84276897 0 +NC_060942.1 80542538 0 +NC_060943.1 61707364 0 +NC_060944.1 66210255 0 +NC_060945.1 45090682 0 +NC_060946.1 51324926 0 +NC_060947.1 154259566 0 +NC_060948.1 62460029 0 +* 0 1 From 42fe1d432f38a017695691381f2193c021e40e57 Mon Sep 17 00:00:00 2001 From: Alexander Dilthey Date: Fri, 6 Dec 2024 16:23:06 +0100 Subject: [PATCH 33/33] Add two new reference specification files --- .../Additional_B38_noALTs_withEBV.txt | 197 ++++++++++++ .../B37_noChr_withViruses.txt | 292 ++++++++++++++++++ 2 files changed, 489 insertions(+) create mode 100644 additionalReferences/PRG_MHC_GRCh38_withIMGT/Additional_B38_noALTs_withEBV.txt create mode 100644 additionalReferences/PRG_MHC_GRCh38_withIMGT/B37_noChr_withViruses.txt diff --git a/additionalReferences/PRG_MHC_GRCh38_withIMGT/Additional_B38_noALTs_withEBV.txt b/additionalReferences/PRG_MHC_GRCh38_withIMGT/Additional_B38_noALTs_withEBV.txt new file mode 100644 index 0000000..253877f --- /dev/null +++ b/additionalReferences/PRG_MHC_GRCh38_withIMGT/Additional_B38_noALTs_withEBV.txt @@ -0,0 +1,197 @@ +contigID contigLength ExtractCompleteContig PartialExtraction_Start PartialExtraction_Stop +chr1 248956422 0 +chr2 242193529 0 +chr3 198295559 0 +chr4 190214555 0 +chr5 181538259 0 +chr6 170805979 0 28510120 33480577 +chr7 159345973 0 +chr8 145138636 0 +chr9 138394717 0 +chr10 133797422 0 +chr11 135086622 0 +chr12 133275309 0 +chr13 114364328 0 +chr14 107043718 0 +chr15 101991189 0 +chr16 90338345 0 +chr17 83257441 0 +chr18 80373285 0 +chr19 58617616 0 +chr20 64444167 0 +chr21 46709983 0 +chr22 50818468 0 +chrX 156040895 0 +chrY 57227415 0 +chrM 16569 0 +chr1_KI270706v1_random 175055 0 +chr1_KI270707v1_random 32032 0 +chr1_KI270708v1_random 127682 0 +chr1_KI270709v1_random 66860 0 +chr1_KI270710v1_random 40176 0 +chr1_KI270711v1_random 42210 0 +chr1_KI270712v1_random 176043 0 +chr1_KI270713v1_random 40745 0 +chr1_KI270714v1_random 41717 0 +chr2_KI270715v1_random 161471 0 +chr2_KI270716v1_random 153799 0 +chr3_GL000221v1_random 155397 0 +chr4_GL000008v2_random 209709 0 +chr5_GL000208v1_random 92689 0 +chr9_KI270717v1_random 40062 0 +chr9_KI270718v1_random 38054 0 +chr9_KI270719v1_random 176845 0 +chr9_KI270720v1_random 39050 0 +chr11_KI270721v1_random 100316 0 +chr14_GL000009v2_random 201709 0 +chr14_GL000225v1_random 211173 0 +chr14_KI270722v1_random 194050 0 +chr14_GL000194v1_random 191469 0 +chr14_KI270723v1_random 38115 0 +chr14_KI270724v1_random 39555 0 +chr14_KI270725v1_random 172810 0 +chr14_KI270726v1_random 43739 0 +chr15_KI270727v1_random 448248 0 +chr16_KI270728v1_random 1872759 0 +chr17_GL000205v2_random 185591 0 +chr17_KI270729v1_random 280839 0 +chr17_KI270730v1_random 112551 0 +chr22_KI270731v1_random 150754 0 +chr22_KI270732v1_random 41543 0 +chr22_KI270733v1_random 179772 0 +chr22_KI270734v1_random 165050 0 +chr22_KI270735v1_random 42811 0 +chr22_KI270736v1_random 181920 0 +chr22_KI270737v1_random 103838 0 +chr22_KI270738v1_random 99375 0 +chr22_KI270739v1_random 73985 0 +chrY_KI270740v1_random 37240 0 +chrUn_KI270302v1 2274 0 +chrUn_KI270304v1 2165 0 +chrUn_KI270303v1 1942 0 +chrUn_KI270305v1 1472 0 +chrUn_KI270322v1 21476 0 +chrUn_KI270320v1 4416 0 +chrUn_KI270310v1 1201 0 +chrUn_KI270316v1 1444 0 +chrUn_KI270315v1 2276 0 +chrUn_KI270312v1 998 0 +chrUn_KI270311v1 12399 0 +chrUn_KI270317v1 37690 0 +chrUn_KI270412v1 1179 0 +chrUn_KI270411v1 2646 0 +chrUn_KI270414v1 2489 0 +chrUn_KI270419v1 1029 0 +chrUn_KI270418v1 2145 0 +chrUn_KI270420v1 2321 0 +chrUn_KI270424v1 2140 0 +chrUn_KI270417v1 2043 0 +chrUn_KI270422v1 1445 0 +chrUn_KI270423v1 981 0 +chrUn_KI270425v1 1884 0 +chrUn_KI270429v1 1361 0 +chrUn_KI270442v1 392061 0 +chrUn_KI270466v1 1233 0 +chrUn_KI270465v1 1774 0 +chrUn_KI270467v1 3920 0 +chrUn_KI270435v1 92983 0 +chrUn_KI270438v1 112505 0 +chrUn_KI270468v1 4055 0 +chrUn_KI270510v1 2415 0 +chrUn_KI270509v1 2318 0 +chrUn_KI270518v1 2186 0 +chrUn_KI270508v1 1951 0 +chrUn_KI270516v1 1300 0 +chrUn_KI270512v1 22689 0 +chrUn_KI270519v1 138126 0 +chrUn_KI270522v1 5674 0 +chrUn_KI270511v1 8127 0 +chrUn_KI270515v1 6361 0 +chrUn_KI270507v1 5353 0 +chrUn_KI270517v1 3253 0 +chrUn_KI270529v1 1899 0 +chrUn_KI270528v1 2983 0 +chrUn_KI270530v1 2168 0 +chrUn_KI270539v1 993 0 +chrUn_KI270538v1 91309 0 +chrUn_KI270544v1 1202 0 +chrUn_KI270548v1 1599 0 +chrUn_KI270583v1 1400 0 +chrUn_KI270587v1 2969 0 +chrUn_KI270580v1 1553 0 +chrUn_KI270581v1 7046 0 +chrUn_KI270579v1 31033 0 +chrUn_KI270589v1 44474 0 +chrUn_KI270590v1 4685 0 +chrUn_KI270584v1 4513 0 +chrUn_KI270582v1 6504 0 +chrUn_KI270588v1 6158 0 +chrUn_KI270593v1 3041 0 +chrUn_KI270591v1 5796 0 +chrUn_KI270330v1 1652 0 +chrUn_KI270329v1 1040 0 +chrUn_KI270334v1 1368 0 +chrUn_KI270333v1 2699 0 +chrUn_KI270335v1 1048 0 +chrUn_KI270338v1 1428 0 +chrUn_KI270340v1 1428 0 +chrUn_KI270336v1 1026 0 +chrUn_KI270337v1 1121 0 +chrUn_KI270363v1 1803 0 +chrUn_KI270364v1 2855 0 +chrUn_KI270362v1 3530 0 +chrUn_KI270366v1 8320 0 +chrUn_KI270378v1 1048 0 +chrUn_KI270379v1 1045 0 +chrUn_KI270389v1 1298 0 +chrUn_KI270390v1 2387 0 +chrUn_KI270387v1 1537 0 +chrUn_KI270395v1 1143 0 +chrUn_KI270396v1 1880 0 +chrUn_KI270388v1 1216 0 +chrUn_KI270394v1 970 0 +chrUn_KI270386v1 1788 0 +chrUn_KI270391v1 1484 0 +chrUn_KI270383v1 1750 0 +chrUn_KI270393v1 1308 0 +chrUn_KI270384v1 1658 0 +chrUn_KI270392v1 971 0 +chrUn_KI270381v1 1930 0 +chrUn_KI270385v1 990 0 +chrUn_KI270382v1 4215 0 +chrUn_KI270376v1 1136 0 +chrUn_KI270374v1 2656 0 +chrUn_KI270372v1 1650 0 +chrUn_KI270373v1 1451 0 +chrUn_KI270375v1 2378 0 +chrUn_KI270371v1 2805 0 +chrUn_KI270448v1 7992 0 +chrUn_KI270521v1 7642 0 +chrUn_GL000195v1 182896 0 +chrUn_GL000219v1 179198 0 +chrUn_GL000220v1 161802 0 +chrUn_GL000224v1 179693 0 +chrUn_KI270741v1 157432 0 +chrUn_GL000226v1 15008 0 +chrUn_GL000213v1 164239 0 +chrUn_KI270743v1 210658 0 +chrUn_KI270744v1 168472 0 +chrUn_KI270745v1 41891 0 +chrUn_KI270746v1 66486 0 +chrUn_KI270747v1 198735 0 +chrUn_KI270748v1 93321 0 +chrUn_KI270749v1 158759 0 +chrUn_KI270750v1 148850 0 +chrUn_KI270751v1 150742 0 +chrUn_KI270752v1 27745 0 +chrUn_KI270753v1 62944 0 +chrUn_KI270754v1 40191 0 +chrUn_KI270755v1 36723 0 +chrUn_KI270756v1 79590 0 +chrUn_KI270757v1 71251 0 +chrUn_GL000214v1 137718 0 +chrUn_KI270742v1 186739 0 +chrUn_GL000216v2 176608 0 +chrUn_GL000218v1 161147 0 +chrEBV 171823 0 +* 0 1 diff --git a/additionalReferences/PRG_MHC_GRCh38_withIMGT/B37_noChr_withViruses.txt b/additionalReferences/PRG_MHC_GRCh38_withIMGT/B37_noChr_withViruses.txt new file mode 100644 index 0000000..91d3c14 --- /dev/null +++ b/additionalReferences/PRG_MHC_GRCh38_withIMGT/B37_noChr_withViruses.txt @@ -0,0 +1,292 @@ +contigID contigLength ExtractCompleteContig PartialExtraction_Start PartialExtraction_Stop +1 249250621 0 +2 243199373 0 +3 198022430 0 +4 191154276 0 +5 180915260 0 +6 171115067 0 28477796 33448355 +7 159138663 0 +8 146364022 0 +9 141213431 0 +10 135534747 0 +11 135006516 0 +12 133851895 0 +13 115169878 0 +14 107349540 0 +15 102531392 0 +16 90354753 0 +17 81195210 0 +18 78077248 0 +19 59128983 0 +20 63025520 0 +21 48129895 0 +22 51304566 0 +X 155270560 0 +Y 59373566 0 +MT 16569 0 +GL000207.1 4262 0 +GL000226.1 15008 0 +GL000229.1 19913 0 +GL000231.1 27386 0 +GL000210.1 27682 0 +GL000239.1 33824 0 +GL000235.1 34474 0 +GL000201.1 36148 0 +GL000247.1 36422 0 +GL000245.1 36651 0 +GL000197.1 37175 0 +GL000203.1 37498 0 +GL000246.1 38154 0 +GL000249.1 38502 0 +GL000196.1 38914 0 +GL000248.1 39786 0 +GL000244.1 39929 0 +GL000238.1 39939 0 +GL000202.1 40103 0 +GL000234.1 40531 0 +GL000232.1 40652 0 +GL000206.1 41001 0 +GL000240.1 41933 0 +GL000236.1 41934 0 +GL000241.1 42152 0 +GL000243.1 43341 0 +GL000242.1 43523 0 +GL000230.1 43691 0 +GL000237.1 45867 0 +GL000233.1 45941 0 +GL000204.1 81310 0 +GL000198.1 90085 0 +GL000208.1 92689 0 +GL000191.1 106433 0 +GL000227.1 128374 0 +GL000228.1 129120 0 +GL000214.1 137718 0 +GL000221.1 155397 0 +GL000209.1 159169 0 +GL000218.1 161147 0 +GL000220.1 161802 0 +GL000213.1 164239 0 +GL000211.1 166566 0 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+HPVTypeMTS1.KY349817.1 7405 0 +HPVTypeRTRX7.U85660.1 7731 0 +HPVTypeXS2.KC138720.1 7830 0 +NC_001436.1 8507 0 +Merkel_cell_polyomavirus.NC_010277.2 5387 0 +NC_000883.2 5596 0 +NC_004102.1 9646 0 +NC_009823.1 9711 0 +NC_009824.1 9456 0 +NC_009825.1 9355 0 +NC_009826.1 9343 0 +NC_009827.1 9628 0 +NC_030791.1 9443 0 +* 0 1 \ No newline at end of file