Added support for bwa-mem2 to the CPU version to speedup the alignmen… #360
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…t 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.
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Added support for bwa-mem2 to the CPU version to speedup the alignment and simplify integration in pipelines already using bwa-mem2 as a main aligner.
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.