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Change of option name and version number
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frederic-mahe committed Jan 30, 2014
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15 changes: 8 additions & 7 deletions swarm.1
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.\" ============================================================================
.TH swarm 1 "30 January 2014" "version 1.2.3" "USER COMMANDS"
.TH swarm 1 "30 January 2014" "version 1.2.4" "USER COMMANDS"
.\" ============================================================================
.SH NAME
swarm \(em find clusters of nearly-identical nucleotide amplicons
Expand Down Expand Up @@ -54,7 +54,7 @@ is "-".
\fBswarm\fR recognizes the following command-line options:
.RS
.TP 9
.BI -b\fP,\fB\ --break_swarms
.BI -b\fP,\fB\ --break-swarms
output all pairs of nearly-identical amplicons to standard error using
a four-columns tab-delimited format: "@@", ampliconA, amplicon B,
number of differences. That option can be used for swarms
Expand Down Expand Up @@ -161,7 +161,7 @@ Submit suggestions and bug-reports at
The software is available from <https://github.com/torognes/swarm>
.\" ============================================================================
.SH COPYRIGHT
Copyright (C) 2012, 2014 Frédéric Mahé & Torbjørn Rognes
Copyright (C) 2012, 2013, 2014 Frédéric Mahé & Torbjørn Rognes
.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
Expand All @@ -185,10 +185,11 @@ Torbjørn Rognes (available from <https://github.com/torognes/swipe>).
New features and important modifications of \fBswarm\fR:
.RS
.TP
.BR v1.2.3\~ "released January 30, 2014"
Version 1.2.3 introduces an option to output all pairs of amplicons to
standard error. The syntax of the inline assembly code is also changed
for compatibility with more compilers.
.BR v1.2.4\~ "released January 30, 2014"
Version 1.2.4 introduces an option --break-swarms to output all pairs
of amplicons with \fId\fR differences to standard error. The syntax of
the inline assembly code is also changed for compatibility with more
compilers.
.TP
.BR v1.2\~ "released May 16, 2013"
Version 1.2 greatly improves speed by using alignment-free comparisons
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