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GATB / bcalm

compacted de Bruijn graph construction in low memory
MIT License
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Option `-out-dir` is not used ? #70

Closed Louis-MG closed 2 years ago

Louis-MG commented 2 years ago

Each run of bcalm I do, I find the *.unitigs.fa in the directory from which I used bcalm, while the .h5 files are in the right place (chosen with -out-dir). I tried finding how to fix it in the .cpp but the option is not present in the commented code of bcalm1 and I couldnt find it in gatb core.

rchikhi commented 2 years ago

hi, yes, -out-dir behavior isn't great. The way to specify where the unitigs.fa file is created is through -out. It's due for a fix some time later. (note to myself: https://github.com/GATB/gatb-core/blob/db4e7da969eec8d432a61d1b09d7ab8ac149f468/gatb-core/src/gatb/debruijn/impl/GraphUnitigs.cpp#L870)