Support for large memory allocations for the genomic repeat analysis tool from Robert Edgar and Eugene Myers.
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Makefile
README.md
annot.cpp
annotedge.cpp
bitfuncs.h
cons.cpp
contigs.cpp
crisp.cpp
findcc.cpp
gff.cpp
gff2.cpp
gffset.cpp
gffset.h
glix.cpp
glix.h
hash.cpp
iix.cpp
iix.h
log.cpp
main.cpp
makeannot.cpp
mem.cpp
options.cpp
params.h
piler2.h
progress.cpp
quit.cpp
readafa.cpp
readhits.cpp
readmfa.cpp
readmotif.cpp
readreps.cpp
readtrs.cpp
tan.cpp
tanmotif2fasta.cpp
tr.cpp
trs.cpp
trs2fasta.cpp
types.h
usage.cpp
utils.cpp
utils_linux.cpp
utils_unix.cpp
utils_win32.cpp
writecrisp.cpp
writefasta.cpp
writeimages.cpp
writepiles.cpp
writetrs.cpp

README.md

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