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Support for large memory allocations for the genomic repeat analysis tool from Robert Edgar and Eugene Myers.

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Makefile
Makefile
 
 
README.md
README.md
 
 
annot.cpp
annot.cpp
 
 
annotedge.cpp
annotedge.cpp
 
 
bitfuncs.h
bitfuncs.h
 
 
cons.cpp
cons.cpp
 
 
contigs.cpp
contigs.cpp
 
 
crisp.cpp
crisp.cpp
 
 
findcc.cpp
findcc.cpp
 
 
gff.cpp
gff.cpp
 
 
gff2.cpp
gff2.cpp
 
 
gffset.cpp
gffset.cpp
 
 
gffset.h
gffset.h
 
 
glix.cpp
glix.cpp
 
 
glix.h
glix.h
 
 
hash.cpp
hash.cpp
 
 
iix.cpp
iix.cpp
 
 
iix.h
iix.h
 
 
log.cpp
log.cpp
 
 
main.cpp
main.cpp
 
 
makeannot.cpp
makeannot.cpp
 
 
mem.cpp
mem.cpp
 
 
options.cpp
options.cpp
 
 
params.h
params.h
 
 
piler2.h
piler2.h
 
 
progress.cpp
progress.cpp
 
 
quit.cpp
quit.cpp
 
 
readafa.cpp
readafa.cpp
 
 
readhits.cpp
readhits.cpp
 
 
readmfa.cpp
readmfa.cpp
 
 
readmotif.cpp
readmotif.cpp
 
 
readreps.cpp
readreps.cpp
 
 
readtrs.cpp
readtrs.cpp
 
 
tan.cpp
tan.cpp
 
 
tanmotif2fasta.cpp
tanmotif2fasta.cpp
 
 
tr.cpp
tr.cpp
 
 
trs.cpp
trs.cpp
 
 
trs2fasta.cpp
trs2fasta.cpp
 
 
types.h
types.h
 
 
usage.cpp
usage.cpp
 
 
utils.cpp
utils.cpp
 
 
utils_linux.cpp
utils_linux.cpp
 
 
utils_unix.cpp
utils_unix.cpp
 
 
utils_win32.cpp
utils_win32.cpp
 
 
writecrisp.cpp
writecrisp.cpp
 
 
writefasta.cpp
writefasta.cpp
 
 
writeimages.cpp
writeimages.cpp
 
 
writepiles.cpp
writepiles.cpp
 
 
writetrs.cpp
writetrs.cpp
 
 

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PILER-64

"PILER is public domain software for analyzing repetitive DNA found in genome sequences." - http://drive5.com/piler/

PILER was originally conceived and implemented by Robert Edgar and Eugene Myers. This derivative version of PILER adds support for 64-bit architectures, and should run to completion without malloc errors on genomes with large, diverse repeat landscapes. Only changes to memory allocation code have been made, so results should be consistent for input data that successfully runs with the version distributed at drive5.com. If you notice discrepencies, please raise an issue here on GitHub.

License

The modifications to PILER distributed here are released to the public domain.

Original License

The PILER software, including object and source code and documentation, is hereby donated to the public domain. Disclaimer of warranty THIS SOFTWARE IS PROVIDED "AS IS" WITHOUT WARRANTY OF ANY KIND, EITHER EXPRESS OR IMPLIED, INCLUDING WITHOUT LIMITATION IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE.

Citing

R.C. Edgar and E.W. Myers, PILER: identification and classification of genomic repeats. Bioinformatics. 2005 Jun 1;21 Suppl 1:i152-i158

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Support for large memory allocations for the genomic repeat analysis tool from Robert Edgar and Eugene Myers.

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