diff options
Diffstat (limited to 'demo/megablast.c')
| -rw-r--r-- | demo/megablast.c | 19 |
1 files changed, 9 insertions, 10 deletions
diff --git a/demo/megablast.c b/demo/megablast.c index 1682d8a6..c012083d 100644 --- a/demo/megablast.c +++ b/demo/megablast.c @@ -1,5 +1,5 @@ -static char const rcsid[] = "$Id: megablast.c,v 6.199 2007/03/20 14:56:58 camacho Exp $"; -/* $Id: megablast.c,v 6.199 2007/03/20 14:56:58 camacho Exp $ +static char const rcsid[] = "$Id: megablast.c,v 6.201 2007/10/23 16:03:23 madden Exp $"; +/* $Id: megablast.c,v 6.201 2007/10/23 16:03:23 madden Exp $ ************************************************************************** * * * COPYRIGHT NOTICE * @@ -26,6 +26,12 @@ static char const rcsid[] = "$Id: megablast.c,v 6.199 2007/03/20 14:56:58 camach * * ************************************************************************** * $Log: megablast.c,v $ + * Revision 6.201 2007/10/23 16:03:23 madden + * No longer set ungapped_extension as an initial word option + * + * Revision 6.200 2007/10/03 17:12:36 papadopo + * do not ignore the value of -H when configuring the current blast engine + * * Revision 6.199 2007/03/20 14:56:58 camacho * Call GeneticCodeSingletonInit/GeneticCodeSingletonFini * @@ -1948,14 +1954,6 @@ BLAST_FillOptions(SBlastOptions* options, Blast_SummaryReturn* sum_returns) lambda*myargs[ARG_XDROP].intvalue/NCBIMATH_LN2, lambda*myargs[ARG_XDROP_FINAL].intvalue/NCBIMATH_LN2); - /* For discontiguous megablast we skip ungapped extensions - when using the 2-hit wordfinder */ - if (lookup_options->mb_template_length > 0) - { - if (word_options->window_size > 0) - word_options->ungapped_extension = FALSE; - } - BLAST_FillHitSavingOptions(hit_options, myargs[ARG_EVALUE].floatvalue, MAX(myargs[ARG_DESCRIPTIONS].intvalue, @@ -1963,6 +1961,7 @@ BLAST_FillOptions(SBlastOptions* options, Blast_SummaryReturn* sum_returns) score_options->gapped_calculation, 0, /* turn off culling */ diag_separation); + hit_options->hsp_num_max = myargs[ARG_MAXHSP].intvalue; if (myargs[ARG_MINSCORE].intvalue) hit_options->cutoff_score = myargs[ARG_MINSCORE].intvalue; |