Command line tool to produce and print pairwise alignments. #739
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Codecov ReportBase: 95.66% // Head: 95.66% // Increases project coverage by
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## main #739 +/- ##
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Coverage 95.66% 95.66%
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Files 125 125
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src/main/scala/com/fulcrumgenomics/personal/tfenne/PairwiseAlign.scala
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| ) extends FgBioTool { | ||
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| override def execute(): Unit = { | ||
| val aligner = Aligner(1, -4, -6, -1, mode) |
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scoring params are hard-coded. Nice to have them exposed on the command line.
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| println() | ||
| println("Right Aligned:") | ||
| right.paddedString().foreach(println) |
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Nice to have the alignment score, cigar, target start/end, query start/end printed too. The latter are useful for local and glocal.
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@nh13 I don't disagree with you suggestions but don't have time to act on them. Shall we merge and can add those later if/when we want? |
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This is here mostly to review
Alignment.revcompedand the associated tests. You're welcome to review the personal tool as well, but I may or may not take feedback there ;)