From 384da11fa5e53944941dcc4b2b329ff04a894f24 Mon Sep 17 00:00:00 2001 From: mahajrod Date: Sat, 19 Oct 2024 13:17:52 +0200 Subject: [PATCH] Added support for bwa-mem2 to the CPU version to speedup the alignment and simplify integration in pipelines already using bwa-mem2 as main alignment. Selection between bwa and bwa-mem2 depends on the presense of the index files: *.bwt.2bit.64 for bwa-mem2 and *.bwt for bwa. First the presence of the bwa-mem2 index is checked. If it is absent test for bwa index is done. --- CPU/juicer.sh | 15 ++++++++++++--- 1 file changed, 12 insertions(+), 3 deletions(-) diff --git a/CPU/juicer.sh b/CPU/juicer.sh index 24b5f7b..841db9a 100755 --- a/CPU/juicer.sh +++ b/CPU/juicer.sh @@ -262,10 +262,19 @@ then fi ## Check that index for refSeq exists - if [[ ! -e "${refSeq}.bwt" ]] + if [[ ! -e "${refSeq}.bwt.2bit.64" ]] then - echo "***! Reference sequence $refSeq does not appear to have been indexed. Please run bwa index on this file before running juicer."; - exit 1; + echo "bwa-mem2 index was not found. Checking if bwa index exists..."; + if [[ ! -e "${refSeq}.bwt" ]] + then + echo "***! Reference sequence $refSeq does not appear to have been indexed. Please run 'bwa index' or 'bwa-mem2 index' on this file before running juicer."; + exit 1; + fi + echo "bwa index was found. Using..."; + bwa_cmd="bwa"; + else + echo "bwa-mem2 index was found. Using..."; + bwa_cmd="bwa-mem2"; fi fi