From 6628a9cf9a6dc6a24d1d9250ca327de8d166e1e9 Mon Sep 17 00:00:00 2001
From: Kevin Lewis <kl2@sanger.ac.uk>
Date: Mon, 26 Jun 2017 16:45:54 +0100
Subject: [PATCH] use bwa aln for human split with tophat target alignment

---
 Changes                                                   | 3 +++
 lib/npg_pipeline/archive/file/generation/seq_alignment.pm | 5 +++--
 2 files changed, 6 insertions(+), 2 deletions(-)

diff --git a/Changes b/Changes
index d38d7427a..a385a575c 100644
--- a/Changes
+++ b/Changes
@@ -1,6 +1,9 @@
 LIST OF CHANGES
 ---------------
 
+release 51.10.2
+ - use bwa aln for human split with tophat target alignment
+
 release 51.10.1
  - Modified qc run function list, removed copy_interop and switched archive_to_irods to samplesheet
  
diff --git a/lib/npg_pipeline/archive/file/generation/seq_alignment.pm b/lib/npg_pipeline/archive/file/generation/seq_alignment.pm
index e84fb6590..731c7f16b 100644
--- a/lib/npg_pipeline/archive/file/generation/seq_alignment.pm
+++ b/lib/npg_pipeline/archive/file/generation/seq_alignment.pm
@@ -313,8 +313,9 @@ sub _lsf_alignment_command { ## no critic (Subroutines::ProhibitExcessComplexity
     $p4_param_vals->{alignment_method} = q[tophat2];
     if($do_target_alignment) { $p4_param_vals->{alignment_reference_genome} = $self->_ref($l,q(bowtie2)); }
     if($nchs) {
-      $p4_param_vals->{hs_alignment_reference_genome} = $self->_default_human_split_ref(q{bowtie2}, $self->repository);
-      $p4_param_vals->{alignment_hs_method} = q[tophat2];
+      # this human split alignment method is currently the same as the default, but this may change
+      $p4_param_vals->{hs_alignment_reference_genome} = $self->_default_human_split_ref(q{bwa0_6}, $self->repository);
+      $p4_param_vals->{alignment_hs_method} = $hs_bwa;
     }
   }
   else {