FindPeaks 3.1.8 (Release candidate) (Apr 18, 2008)
This is not a final release. Experimental releases should only be used for testing and development. Do not use these on production sites, and make sure you have proper backups before installing.
Bugfix version, more compatibiity with alternate pipelines.
For additional information about this project, please visit the overview page .
Available downloads
AlignSlice - a program for creating viewer-ready files for small "slices" of a genome.
For all platforms (17.4 KB)
ElandToBed - creates a gzipped bed file for viewing eland files with the UCSC browser
For all platforms (11.5 KB)
VulgarToBed - creates gzipped UCSC bed files from Vulgar (Exonerate) format files
For all platforms (11.8 KB)
Release Notes
| State | Release candidate |
|---|---|
| License | BCCA |
| Release Manager | Anthony Fejes |
This version solves many issues experienced by user inside and outside of the BCGSC. It should provide error checking of paramters supplied at run time, and improve the ability to identify the chromosome names in a manner compatible with the UCSC browser. See change log for list of core changes.
Change log
Changelog since version 3.1.6 for findpeaks.java (does not include libraries and modules.)
* Enhancement: Vulgar Iterator now replaces defunct ElandIterator
* Enhancement: Eland Extended Iterator roughed in. Not yet functional.
* Enhancement: default -dist_type is now set to 1 (Triangle distribution.)
* Enhancement: Added flag to turn on/off header line in peaks files.
* Refactor: instead of collecting statistics in 3 locations, now do it all while writing out to peaks file.
* Enhancement: Prevent use case where -subpeaks value is higher than -trim value. While it *could* be a legitimate use case, it's not the desired case (after consultation with Nina), and would require a rewrite to the code handling this case. [resolves IJT-17]
* Enhancement: -minimum (minPeak) can now be provided as a float value, instead of an integer. Resolves IJT-12.
* Bugfix: peak start and peak end were incorrect for case with -subpeaks on, but -trim off. Relative positions were being supplied by the findmin() function, and not converted to absolute positions. This has now been fixed. Resovles IJT-1.
* bugfix for issue IJT-11. Now processes chromosomes with unknown names, and gives warning.
* Enhancement: only check chromosome name once per peaklocator run.
* BugFix: with subpeaks off, end should still be an absolute coordinate.
* default value now specified for "scanned_value". (We aren't pre-scanning anymore, so this needs to be provided.)
* Genome size must not be zero for Rmode
* group together all R writing functions.
* clean up R file, (no more text, and removed grey line at end of graphic.
