bugs in r2302

[congmao wang]

OS:

Ubuntu 12.04.4 LTS

3.2.0-23-generic #36-Ubuntu SMP Tue Apr 10 20:39:51 UTC 2012 x86_64 x86_64 x86_64 GNU/Linux

read_fastq -i $BP_DIR/bp_test/in/read_fastq.in.2 -O $BP_TMP/congmao.read_fastq.out

/home/congmao/Desktop/bitbucket/parse_options/utilities/biopieces/share/biopieces/code_ruby/lib/maasha/seq.rb:610:in `qual_convert_C': integer -31 too small to convert to `unsigned int' (RangeError)

from biopieces/code_ruby/lib/maasha/seq.rb:610:in `qual_convert!'

from biopieces/bp_bin/read_fastq:119:in `block (4 levels) in <main>'

from biopieces/code_ruby/lib/maasha/filesys.rb:104:in `each'

from biopieces/bp_bin/read_fastq:108:in `block (3 levels) in <main>'

from biopieces/code_ruby/lib/maasha/filesys.rb:76:in `open'

from biopieces/bp_bin/read_fastq:107:in `block (2 levels) in <main>'

from biopieces/bp_bin/read_fastq:106:in `each'

from biopieces/bp_bin/read_fastq:106:in `block in <main>'

from biopieces/code_ruby/lib/maasha/biopieces.rb:89:in `open'

from biopieces/bp_bin/read_fastq:51:in `<main>'

read_fastq -i $BP_DIR/bp_test/in/read_fastq.in.2 -e base_64 -O $BP_TMP/congmao.read_fastq.out

/home/congmao/Desktop/bitbucket/parse_options/utilities/biopieces/share/biopieces/code_ruby/lib/maasha/seq.rb:610:in `qual_convert_C': integer -31 too small to convert to `unsigned int' (RangeError)

from biopieces/code_ruby/lib/maasha/seq.rb:610:in `qual_convert!'

from biopieces/bp_bin/read_fastq:119:in `block (4 levels) in <main>'

from biopieces/code_ruby/lib/maasha/filesys.rb:104:in `each'

from biopieces/bp_bin/read_fastq:108:in `block (3 levels) in <main>'

from biopieces/code_ruby/lib/maasha/filesys.rb:76:in `open'

from biopieces/bp_bin/read_fastq:107:in `block (2 levels) in <main>'

from biopieces/bp_bin/read_fastq:106:in `each'

from biopieces/bp_bin/read_fastq:106:in `block in <main>'

from biopieces/code_ruby/lib/maasha/biopieces.rb:89:in `open'

from biopieces/bp_bin/read_fastq:51:in `<main>'

[Martin Asser Hansen]

OK, I changed a unsigned int to int to accomodate the -31 value and this should then be fixed. bp_update && bp_test

Cheers,

Martin

--
You received this message because you are subscribed to the Google Groups "biopieces" group.
To unsubscribe from this group and stop receiving emails from it, send an email to biopieces+...@googlegroups.com.
For more options, visit https://groups.google.com/d/optout.

[congmao wang]

unfortunately, it still fails. Please see the following:

read_fastq -i $BP_DIR/bp_test/in/read_fastq.in.2 -O $BP_TMP/congmao.read_fastq.out

/biopieces/code_ruby/lib/maasha/seq.rb:610:in `qual_convert_C': integer -31 too small to convert to `unsigned int' (RangeError)

        from /biopieces/code_ruby/lib/maasha/seq.rb:610:in `qual_convert!'
        from /biopieces/bp_bin/read_fastq:119:in `block (4 levels) in <main>'
        from /biopieces/code_ruby/lib/maasha/filesys.rb:104:in `each'
        from /biopieces/bp_bin/read_fastq:108:in `block (3 levels) in <main>'
        from /biopieces/code_ruby/lib/maasha/filesys.rb:76:in `open'
        from /biopieces/bp_bin/read_fastq:107:in `block (2 levels) in <main>'
        from /biopieces/bp_bin/read_fastq:106:in `each'
        from /biopieces/bp_bin/read_fastq:106:in `block in <main>'
        from /biopieces/code_ruby/lib/maasha/biopieces.rb:89:in `open'
        from /biopieces/bp_bin/read_fastq:51:in `<main>'

read_fastq -i $BP_DIR/bp_test/in/read_fastq.in.2 -e base_64 -O $BP_TMP/congmao.read_fastq.out

/biopieces/code_ruby/lib/maasha/seq.rb:610:in `qual_convert_C': integer -31 too small to convert to `unsigned int' (RangeError)

        from /biopieces/code_ruby/lib/maasha/seq.rb:610:in `qual_convert!'
        from /biopieces/bp_bin/read_fastq:119:in `block (4 levels) in <main>'
        from /biopieces/code_ruby/lib/maasha/filesys.rb:104:in `each'
        from /biopieces/bp_bin/read_fastq:108:in `block (3 levels) in <main>'
        from /biopieces/code_ruby/lib/maasha/filesys.rb:76:in `open'
        from /biopieces/bp_bin/read_fastq:107:in `block (2 levels) in <main>'
        from /biopieces/bp_bin/read_fastq:106:in `each'
        from /biopieces/bp_bin/read_fastq:106:in `block in <main>'
        from /biopieces/code_ruby/lib/maasha/biopieces.rb:89:in `open'
        from /biopieces/bp_bin/read_fastq:51:in `<main>'

Cheers,
Congmao

[Martin Asser Hansen]

So these tests pass on my Mac and our server (r2310). There must be some differences with how inline code is complied and cached on mac, debian and ubuntu.

However, after inspecting the code I found a small snag (changing a UINT2FIX macro to INT2FIX), which is now fixed. I hope this solves the problem?

bp_update && bp_test

Cheers,

Martin

--

[congmao wang]

Great, 10 times test, all pass:)

cheers,

Congmao