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PR/43777 CVS commit: pkgsrc/biology/lucy

The following reply was made to PR pkg/43777; it has been noted by GNATS.

From: OBATA Akio <>
Subject: PR/43777 CVS commit: pkgsrc/biology/lucy
Date: Sun, 19 Sep 2010 07:13:37 +0000

 Module Name:   pkgsrc
 Committed By:  obache
 Date:          Sun Sep 19 07:13:37 UTC 2010
 Modified Files:
        pkgsrc/biology/lucy: Makefile distinfo
 Log Message:
 Update lucy to 1.20.
 Based on PR#43777 by Kamel Derouiche, with some clean up by me.
 Version 1.20, 9/3/2008.  This version fixes a bug that caused lucy
 to fail when there was too much information on the FASTA header lines
 in the input files.  Lucy had a 256 character buffer for reading
 lines from the input files.  If any FASTA header lines were longer
 than 256 characters, the remaining characters would get read as part
 of the FASTA sequence.  The solution implemented in this version is
 simply to increase the buffer size to 4096 characters.  While that
 still leaves the potential for the same error to occur with extremely
 long header lines, the limitation that this entails seems reasonable,
 and this should fix the problem for all pratical purposes.
 Version 1.19, 12/30/2003.  This version fixes a bug that could cause
 sequences to be rejected incorrectly in the vector detection step
 (phase 6).  Because of the way that lucy compares "tags" in the
 target sequence with "tags" in the vector sequence, some bases in
 the target sequence could get counted more than once in the tally
 of bases that match the vector sequence.  In rare instances, this
 could cause the sequence to exceed the minimum threshold for
 rejection, as a result of random sequence similarity.
 The reporting of the CLB range in the -debug output file has also
 been changed.  If the CLB range begins with the first base of the
 sequence, then the left coordinate of the CLB range will be reported
 as 1 (instead of 0).  The range "CLB 0 0" still indicates an empty
 CLB range.
 To generate a diff of this commit:
 cvs rdiff -u -r1.6 -r1.7 pkgsrc/biology/lucy/Makefile
 cvs rdiff -u -r1.3 -r1.4 pkgsrc/biology/lucy/distinfo
 Please note that diffs are not public domain; they are subject to the
 copyright notices on the relevant files.

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