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README.md

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ROOT scripts to convert a SAM file to a RAM (ROOT Alignment/Map) file and to work on RAM files.

  • To convert a SAM file to a RAM file do:
  $ root
  root [0] .x samtoram.C
  root [1] .q
  • To test read a RAM file do:
    $ root
    root [0] .x ramreader.C
    root [1] .q
  • To view a region, the equivalent of samtools view bamexample.bam chr1:10150-10300, do:
    $ root
    root [0] .x ramview.C("ramexample.root","chr1:10150-10300")
    root [1] .q