Dev #115
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Dev #115
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The keyword `physcov`in pileup counts the bases between correctly mapped, not overlapping paired-end reads as covered. I think this is a great feature but it is incopatibl with asking bbmap to map to all ambigous sites `ambigous=all`
Contigs should be filtered based on all possible mappings. As we have the option in the `align_reads_to_final_contigs` we should filter contigs based on all ambigous mapping results and not only on the best (default).
… assembly/logs to logs/assembly
merged reads are used sperately by spades. added possibility to drop normalization
made filtering optional not tested
Spades 3.12
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contains all changes for now found in #114 #102 #111
I'm testing this branch