Daniel Shahaf wrote on Wed, Jan 18, 2017 at 15:22:26 +0000:
> The attached patch should fix both issues.
--- a/doc/hhsuite-userguide.tex
+++ b/doc/hhsuite-userguide.tex
@@ -1466,7 +1466,7 @@
-maxfilt max number of hits allowed to pass 2nd prefilter
(default=20000)
-min_prefilter_hits min number of hits to pass prefilter (default=100)
-prepre_smax_thresh min score threshold of ungapped prefilter
(default=10)
- -pre_evalue_thresh max E-value threshold of Smith-Waterman prefilter
score (default=0)
+ -pre_evalue_thresh max E-value threshold of Smith-Waterman prefilter
score (default=1000.0)
-pre_bitfactor prefilter scores are in units of 1 bit /
pre_bitfactor (default=4)
-pre_gap_open gap open penalty in prefilter Smith-Waterman
alignment (default=20)
-pre_gap_extend gap extend penalty in prefilter Smith-Waterman
alignment (default=4)
--- a/src/hhblits.cpp
+++ b/src/hhblits.cpp
@@ -330,7 +330,7 @@
printf(" -maxfilt max number of hits allowed to pass 2nd
prefilter (default=%i) \n", par.maxnumdb);
printf(" -min_prefilter_hits min number of hits to pass prefilter
(default=%i) \n", par.min_prefilter_hits);
printf(" -prepre_smax_thresh min score threshold of ungapped
prefilter (default=%i) \n", par.preprefilter_smax_thresh);
- printf(" -pre_evalue_thresh max E-value threshold of Smith-Waterman
prefilter score (default=%i)\n", par.prefilter_evalue_thresh);
+ printf(" -pre_evalue_thresh max E-value threshold of Smith-Waterman
prefilter score (default=%.1f)\n", par.prefilter_evalue_thresh);
printf(" -pre_bitfactor prefilter scores are in units of 1 bit
/ pre_bitfactor (default=%i)\n", par.prefilter_bit_factor);
printf(" -pre_gap_open gap open penalty in prefilter
Smith-Waterman alignment (default=%i)\n", par.prefilter_gap_open);
printf(" -pre_gap_extend gap extend penalty in prefilter
Smith-Waterman alignment (default=%i)\n", par.prefilter_gap_extend);
