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PengNi / basemods_spark

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suffixArrayFile for a reference #2

Closed PengNi closed 6 years ago

PengNi commented 6 years ago

when aligning, if the reference does not have a suffixArrayFile 'sa' file, need to use the sawriter program in BLASR to generate it.

in the spark pipeline, we have to let users to choose if they provide the 'fasta.sa' file or not. if they don't provide, we write the code in the pipeline to cal it automatically.

PengNi commented 6 years ago

finished it at commit add sawriter process