diff --git a/doc/vsearch.1 b/doc/vsearch.1 index 11677425..e3e7ab72 100644 --- a/doc/vsearch.1 +++ b/doc/vsearch.1 @@ -1,5 +1,5 @@ .\" ============================================================================ -.TH vsearch 1 "January 22, 2015" "version 1.0.9" "USER COMMANDS" +.TH vsearch 1 "January 23, 2015" "version 1.0.10" "USER COMMANDS" .\" ============================================================================ .SH NAME vsearch \(em chimera detection, clustering, dereplication, masking, pairwise alignment, searching, shuffling and sorting of amplicons from metagenomic projects. @@ -434,7 +434,7 @@ just a decreasing length ordering. .TP Most searching options also apply to clustering: .br ---alnout, --blast6out, --userout, --userfields, fastapairs, --matched, +--alnout, --blast6out, --userout, --userfields, --fastapairs, --matched, --notmatched, --maxaccept, --maxreject, score filtering, gap penalties, masking. (see the Searching section). .RE .PP @@ -684,7 +684,7 @@ or positive integers, and "/" is used as a separator. .br To simplify declarations, the location symbols (L, I, and R) can be combined, the symbol (E) can be used to treat both extremities (L and -R) equally, and the symbols Q and T can be ommited to treat query and +R) equally, and the symbols Q and T can be omitted to treat query and target sequences equally. For instance, the default is to declare a penalty of 20 for opening internal gaps and a penalty of 2 for opening terminal gaps (left or right), in both query and target sequences @@ -1381,7 +1381,7 @@ curmudgeont e-mail to Torbjørn Rognes . Source code and binaries are available at . .\" ============================================================================ .SH COPYRIGHT -Copyright (C) 2014, 2015 Torbjørn Rognes and collaborators. +Copyright (C) 2014, 2015 Torbjørn Rognes, Frédéric Mahé and Tomas Flouri. .PP This program is free software: you can redistribute it and/or modify it under the terms of the GNU Affero General Public License as @@ -1482,6 +1482,10 @@ fix for lack of detection of under- or overflow in SIMD aligner. .TP .BR v1.0.9\~ "released January 22nd, 2015" Fixes a bug in the function sorting sequences by decreasing abundance (--sortbysize). +.TP +.BR v1.0.10\~ "released January 23rd, 2015" +Fixes a bug where the sizein option was ignored and always treated as on, +affecting clustering and dereplication commands. .LP .\" ============================================================================ .\" TODO: diff --git a/doc/vsearch_manual.pdf b/doc/vsearch_manual.pdf index fb63b7de..fd2b92c4 100644 Binary files a/doc/vsearch_manual.pdf and b/doc/vsearch_manual.pdf differ