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add adam view command, analogous to samtools view #451

Merged
merged 7 commits into from
Nov 7, 2014
Merged

add adam view command, analogous to samtools view #451

merged 7 commits into from
Nov 7, 2014

Commits on Nov 5, 2014

  1. helper to get SAM output as a string

    @ryan-williams
    ryan-williams committed Nov 5, 2014
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  2. add adam view command 

    similar to `samtools view`
    @ryan-williams
    ryan-williams committed Nov 5, 2014
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  3. add -c, -o flags, plus opt. printing SAM to stdout

    @ryan-williams
    ryan-williams committed Nov 5, 2014
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  4. add "disjunction" -g / -G options to adam view 

    -f and -F do positive and negative conjunctions, but in at least one
situation I've wanted to do an "or": give me all reads in this file
where the read is unmapped *or* the mate is unmapped.
    @ryan-williams
    ryan-williams committed Nov 5, 2014
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  5. expose non-file-saving bits of adam transform

    @ryan-williams
    ryan-williams committed Nov 5, 2014
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  6. expose non-file-saving bits of adam view

    @ryan-williams
    ryan-williams committed Nov 5, 2014
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  7. Add a test for new view command 

    - includes a SAM file with one read for each of the 700 possible
  flag-field values allowed by HTSJDK’s and ADAM’s SAM parsing code
  paths.
- bonus: includes `make-flag-values-sam.py` script used to generate the
  aforementioned SAM file.
- concern: ViewSuite test takes about 30s to run on my laptop; how much
  do we care about test-running latency? Is there an obviously quicker
  way to run a similar test to what I have here?
    @ryan-williams
    ryan-williams committed Nov 5, 2014
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