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Revision history for diffReps.
1.55.4 Wed Sep 25 2013
- Some code re-written (added DEBUG directive).
- Fixed a bug introduced in v1.55.3 which can cause temporary chromosome
files to be deleted prematurely when more than one processes are used.
- Strengthened the reliability against exceptions.
1.55.3 Thu Sep 12 2013
- diffReps will now remove intermediate files even if it dies from
exceptions.
- The POD of diffReps modules are re-written so that they are more
informative.
- Use Perl built-in functions to delete intermediate files instead of
external "rm" in the main program, making it more friendly to Windows
users.
- Corrected some version numbers.
1.55.2 Sat Aug 31 2013
- Corrected some mistakes in Makefile.PL.
- Made the program aware of the number of required replicates when nb and
tt are selected.
1.55 Wed Jun 26 2013
- Allow chromosome names to have more flexible format.
- added example/norm.txt.
1.54 Fri Nov 2 2012
- A quick-and-dirty implementation of parallel processing.
- findHotspots now accepts option to specify columns to extract.
- New default values for option "--nsd": broad(2) and sharp(20) peaks.
- Column "logFC" is renamed to "log2FC" to avoid any ambiguity.
1.43 Mon Jul 23 2012
- The null model used in findHotspot has been changed to local Poisson.
- Added support for background samples, such as DNA input or IgG, to
calculate enrichment for each differential site.
- Filter windows based on background enrichment (using this can make
detection >2 times slower).
- Misc. improvement to make detecting differential sites more efficient
(~70% faster).
1.33 Tue Jun 19 2012
- Output average read count for each site for further filtering purpose.
- Output diffReps version and full command used.
1.32 Fri Mar 23 2012
- Added script and database files for automatic annotation of differential
sites.
- Added script to look for chromatin modification hotspots from diffReps
results.
1.12 Thu Mar 22 2012
- Added robust estimation for background mean and deviation. Right-trimmed
mean is used to replace arithmetic average. Median absolute deviation is
used to replace standard deviation.
- Robust estimation is done on a sub-sample of 100,000 bins instead of the
whole genome to save compuational cost and memory usage.
1.02 Thu Mar 8 2012
- fixed a bug that will generate a warning message if you provide your own
chromosome length file.
- added a routine to choose window and step size more sensiblely and prevent
weird values.
1.01 Fri Mar 2 2012
- fixed a tiny bug that will generate a warning message if round-off errors
cause the G-statistic to be a negative.
- added scripts to convert from ELAND and SAM alignment to BED files.
- added a script to remove redundant short reads.
1.00 Wed Feb 29 2012
- a workable version created and tested.
0.01 Sat Feb 25 15:49:37 2012
- original version; created by h2xs 1.23 with options
- AX -b 5.6.0 -n diffReps