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Commits on Sep 11, 2012
  1. "user-destdir" is default these days

    asau committed
Commits on Sep 19, 2010
  1. Update lucy to 1.20.

    obache committed
    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.
Commits on Jun 14, 2009
  1. Remove @dirrm entries from PLISTs

    joerg committed
Commits on Jun 12, 2009
  1. Made the Makefile simpler.

    rillig committed
    Removed unnecessary .gz suffix from man pages.
Commits on May 16, 2009
  1. update homepage, update master site.

    zafer committed
Commits on Mar 3, 2008
  1. Mechanical changes to add full DESTDIR support to packages that install

    jlam committed
    their files via a custom do-install target.
Commits on Jan 7, 2007
  1. Mechanically replaced man/* with ${PKGMANDIR}/* in the definition of

    rillig committed
    INSTALLATION_DIRS, as well as all occurrences of ${PREFIX}/man with
    ${PREFIX}/${PKGMANDIR}.
    
    Fixes PR 35265, although I did not use the patch provided therein.
Commits on Oct 4, 2006
Commits on Dec 13, 2005
  1. Don't hard-wire -lpthread, use PTHREAD_*.

    joerg committed
Commits on May 25, 2005
  1. Add RMD160 checksum.

    wiz committed
Commits on Mar 26, 2005
  1. Import lucy from pkgsrc-wip. Packaged by David Price and modified by me.

    minskim committed
    A Sequence Cleanup Program.  Lucy is a utility that prepares raw DNA
    sequence fragments for sequence assembly,possibly using the TIGR
    Assembler.  The cleanup process includes quality assessment,
    confidence reassurance, vector trimming and vector removal.  The
    primary advantage of Lucy over other similar utilities is that it is a
    fully integrated, stand alone program.
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