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LAST is not outputting MAF in the sense of MIRA Alignment Format (which is what my tool maf2sam.py converts into SAM/BAM).
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LAST output as SAM/BAM
Im testing the sequence read mapping LAST (http://last.cbrc.jp/) But this program only outputs MAF alignment files. I tried using https://github.com/peterjc/maf2sam to convert to SAM/BAM but I get the following error:
command:
Code:python maf2sam.py reference.fa al.maf
Code:[maf2sam] Identified 0 read groups Traceback (most recent call last): File "maf2sam.py", line 514, in <module> assert line.startswith("CO\t"), line AssertionError: # fraglen=217.0 sdev=146.778 disjoint=0.01 genome=6264404
? Thanks
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