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bioperl-l@bioperl.org - General discussion
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http://bioperl.org/wiki/Mailing_lists - About the mailing lists
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Please direct usage questions or support issues to the mailing list:
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I<bioperl-l@bioperl.org>
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rather than to the module maintainer directly. Many experienced and
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reponsive experts will be able look at the problem and quickly
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address it. Please include a thorough description of the problem
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with code and data examples if at all possible.
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=head2 Reporting Bugs
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Report bugs to the Bioperl bug tracking system to help us keep track
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'BlastOutput_version' => 'RESULT-algorithm_version',
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'BlastOutput_db' => 'RESULT-database_name',
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'BlastOutput_reference' => 'RESULT-program_reference',
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'Parameters_matrix' => { 'RESULT-parameters' => 'matrix'},
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'Parameters_expect' => { 'RESULT-parameters' => 'expect'},
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'Parameters_include' => { 'RESULT-parameters' => 'include'},
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'Parameters_sc-match' => { 'RESULT-parameters' => 'match'},
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'Parameters_sc-mismatch' => { 'RESULT-parameters' => 'mismatch'},
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'Parameters_gap-open' => { 'RESULT-parameters' => 'gapopen'},
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'Parameters_gap-extend'=> { 'RESULT-parameters' => 'gapext'},
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'Parameters_filter' => {'RESULT-parameters' => 'filter'},
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'Statistics_db-num' => 'RESULT-database_entries',
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'Statistics_db-len' => 'RESULT-database_letters',
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'Statistics_hsp-len' => { 'RESULT-statistics' => 'hsplength'},
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'Statistics_eff-space' => { 'RESULT-statistics' => 'effectivespace'},
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'Statistics_kappa' => { 'RESULT-statistics' => 'kappa' },
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'Statistics_lambda' => { 'RESULT-statistics' => 'lambda' },
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'Statistics_entropy' => { 'RESULT-statistics' => 'entropy'},
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'BlastOutput_query-def' => 'RESULT-query_description',
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'BlastOutput_query-len' => 'RESULT-query_length',
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'BlastOutput_query-ID' => 'runid',
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'BlastOutput_query-ID' => 'runid',
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'Parameters_matrix' => { 'RESULT-parameters' => 'matrix'},
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'Parameters_expect' => { 'RESULT-parameters' => 'expect'},
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'Parameters_include' => { 'RESULT-parameters' => 'include'},
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'Parameters_sc-match' => { 'RESULT-parameters' => 'match'},
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'Parameters_sc-mismatch' => { 'RESULT-parameters' => 'mismatch'},
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'Parameters_gap-open' => { 'RESULT-parameters' => 'gapopen'},
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'Parameters_gap-extend' => { 'RESULT-parameters' => 'gapext'},
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'Parameters_filter' => {'RESULT-parameters' => 'filter'},
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'Statistics_db-num' => 'RESULT-database_entries',
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'Statistics_db-len' => 'RESULT-database_letters',
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'Statistics_hsp-len' => { 'RESULT-statistics' => 'hsplength'},
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'Statistics_eff-space' => { 'RESULT-statistics' => 'effectivespace'},
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'Statistics_kappa' => { 'RESULT-statistics' => 'kappa' },
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'Statistics_lambda' => { 'RESULT-statistics' => 'lambda' },
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'Statistics_entropy' => { 'RESULT-statistics' => 'entropy'},
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# HSP specific fields
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'Hsp_bit-score' => 'HSP-bits',
added
removed
Bio/SearchIO/XML/BlastHandler.pm
