[Biojava-dev] [Bug 2407] New: BlastParser cannot parse the result of blastall using '-n' (MegaBlast Search) argument

[bugzilla-daemon at portal.open-bio.org]

http://bugzilla.open-bio.org/show_bug.cgi?id=2407

           Summary: BlastParser cannot parse the result of blastall using '-
                    n' (MegaBlast Search) argument
           Product: BioJava
           Version: 1.5
          Platform: All
        OS/Version: All
            Status: NEW
          Severity: critical
          Priority: P1
         Component: seq
        AssignedTo: biojava-dev at biojava.org
        ReportedBy: iridiumcao at gmail.com


There is a problem to parse the output result of blastall using the argument
'-n' (MegaBlast Search). The query sequence ID and hit-start/end positions are
inconsistent with the blast result text.

Two blastall output files are attached, one is generated by blastall not using
the argument '-n' (MegaBlast Search),  parsed correctly; the other is generated
using the argument '-n' (MegaBlast Search), parsed woronglg.


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