[Biojava-dev] [Bug 2584] New: Parsing blast result only returns hits from first query sequence

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

http://bugzilla.open-bio.org/show_bug.cgi?id=2584

           Summary: Parsing blast result only returns hits from first query
                    sequence
           Product: BioJava
           Version: unspecified
          Platform: PC
        OS/Version: Windows XP
            Status: NEW
          Severity: normal
          Priority: P2
         Component: bio
        AssignedTo: biojava-dev at biojava.org
        ReportedBy: dtoomey at rcsi.ie


Hi

When parsing a blast result containing multiple query sequences I have found
that only the hits from the first query are returned in the array list. The
source code is taken directly from the cookbook. If the first query hits are
deleted from the file then the second query sequence hits are returned. So it
does not appear to be something specific to the result for that sequence that
prevents it from being parsed correctly.
I am using biojava 1.6 and blast 2.2.18. I have tried it with blast 2.2.14 and
2.2.16 and I get the same problem


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