Commits on Jul 8, 2021

1. Speed up BAM, CRAM 3.1 and 4.0 testing in test/test.pl's test_view. …

   Many of the SAM test files cover corner cases that don't change with
   3.1 or 4.0, so we don't need to rerun every test in every format
   variation.  Additionally we don't need to use compression for every
   test using BAM.
   
   These have been tested using gcov to validate the total code coverage
   doesn't change.
   
   - Only run 3.1/4.0 tests on a subset of SAM files.
   
   - Only test 3.1/4.0 when running with threads. (Second call to
     test_view).  TODO: Likely this could be applied to 3.0 tests too to
     limit which files are tested in a threaded environment.
   
   - Drop some of the 2.1 tests.  If we can go from SAM -> 2.1 -> SAM
     then it's good enough to validate encode and decode, with no need
     for 2.1 to 3 interchange checks.
   
   - Drop some of the 3.0/3.1/4.0 interchange tests.  As with 2.1, we
     only need to know we can go to/from a common SAM format to test the
     code paths.
   
   - Don't test compressed BAM on all files.  1 is enough, and then
     uncompressed for the rest (lvl 1).
   
   - Don't test uncompressed CRAM on all files.  Just do it for 1.  We do
     want compressed mostly though as CRAM has a lot of codecs to explore.
   
   - No Point in BAM -> CRAM -> BAM -> SAM when BAM -> CRAM -> SAM is
     sufficient.
   
   - Drop the multi-ref CRAM testing for v3.1 and v4.0 as it's the same
     code path tested in v3.0 anyway.  This does change coverage
     marginally, but it's trivial (3 lines reallocing MD in cram_decode.c).
   
   - Only do multi-ref CRAM testing on CRAM files with > 1 ref and when
     threaded. (Albeit with a minor 2 line testing differnce to cram_io.c.)
   
   - Reduce the number of CRAM profiles tested.  Do full 4 profiles on
     one file per v3.1 and v4.0.  Otherwise a single profile.
   
   The inpact of this is time spent in the test_view subroute drops from
   
       real    2m3.525s
       user    1m20.362s
       sys     0m26.804s
   
   to
   
       real    0m21.618s
       user    0m12.925s
       sys     0m4.148s
   
   This single function dominated all testing (which on the same system
   took 2m37s for the entire test suite), so the impact on overall time
   is considerable.

   

   jkbonfield committed Jul 8, 2021
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