Bio::Tools::Run::BWA failing tests

[cjfields]

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Author Name: Chris Fields (@cjfields)
Original Redmine Issue: 3210, https://redmine.open-bio.org/issues/3210
Original Date: 2011-04-19
Original Assignee: Bioperl Guts

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I have TODO’d the assembly pipeline tests for t/BWA.t in bioperl-run master branch, these are failing with the latest bwa (may be version inconsistencies).

cjfields@pyrimidine:~/bioperl/bioperl-run$ bwa

Program: bwa (alignment via Burrows-Wheeler transformation)
Version: 0.5.9-r16
Contact: Heng Li 

Usage:   bwa  [options]

Command: index         index sequences in the FASTA format
         aln           gapped/ungapped alignment
         samse         generate alignment (single ended)
         sampe         generate alignment (paired ended)
         bwasw         BWA-SW for long queries

         fa2pac        convert FASTA to PAC format
         pac2bwt       generate BWT from PAC
         pac2bwtgen    alternative algorithm for generating BWT
         bwtupdate     update .bwt to the new format
         pac_rev       generate reverse PAC
         bwt2sa        generate SA from BWT and Occ
         pac2cspac     convert PAC to color-space PAC
         stdsw         standard SW/NW alignment

cjfields@pyrimidine:~/bioperl/bioperl-run$ t t/BWA.t 
t/BWA.t .. 
1..36
ok 1 - make a factory using command 'aln'
ok 2 - parameters changed on construction
ok 3 - access parameter
ok 4 - parameters_changed cleared on read
ok 5 - set a param not set in constructor
ok 6 - parameters_changed set
ok 7 - parameter really set
ok 8 - original parameter unchanged
ok 9 - parameters_changed cleared on read
ok 10 - change an original parameter
ok 11 - parameter really changed
ok 12 - reset parameters with arg
ok 13 - original parameters undefined
ok 14 - parameter really reset via arg
ok 15 - parameters changed
ok 16 - all available options
ok 17 - available parameters
ok 18 - available switches
ok 19 - get_parameters correct
ok 20 - command attribute set
ok 21 - internal command array set
ok 22 - internal prefix hash set
ok 23 - commands filtered by prefix
ok 24 - translate params
ok 25 - make refseq index factory
ok 26 - index refseq
ok 27 - make aln factory
ok 28 - map read1 to refseq
ok 29 - map read 2 to refseq
ok 30 - paired read assembly factory
ok 31 - assemble paired reads
ok 32 - make a full assembly factory
ok 33 - command attribute set
[bam_parse_region] invalid region.
[bam_parse_region] invalid region.

--------------------- WARNING ---------------------
MSG: Got a sequence with no letters in it cannot guess alphabet
---------------------------------------------------

--------------------- WARNING ---------------------
MSG: Got a sequence with no letters in it cannot guess alphabet
---------------------------------------------------
ok 34 - make full assy
not ok 35 - number of contigs # TODO latest bwa doesn't work with assembly pipeline

#   Failed (TODO) test 'number of contigs'
#   at t/BWA.t line 109.
#          got: '419'
#     expected: '204'
not ok 36 - number of singlets # TODO latest bwa doesn't work with assembly pipeline

#   Failed (TODO) test 'number of singlets'
#   at t/BWA.t line 110.
#          got: '15'
#     expected: '220'
ok
All tests successful.
Files=1, Tests=36,  6 wallclock secs ( 0.03 usr  0.01 sys +  6.50 cusr  0.22 csys =  6.76 CPU)
Result: PASS