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Changelog
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December 19, 2018:
version 1.1.3:
* A corner case bug is fixed.
November 30, 2018:
version 1.1.2:
* Memory leak in gene copy number calculation is fixed.
November 28, 2018:
version 1.1.1:
* Dry run and "cloud mode" added to mrcanavar-auto.
November 27, 2018:
version 1.1:
* mrcanavar-auto added for automated mapping & calling. Assumes that some files are available in the working directory. Use it with caution.
November 20, 2018:
version 1.0:
* SAM(.gz) files in READ mode can now be passed as comma-separated list.
April 18, 2014:
version 1.0 beta:
* GC normalization is now less strict
* Duplication windows are calculated through LW and SW. CW info for further filtering to be added.
September 4, 2013:
version 0.51 released:
* No new updates, only the bugfix below.
July 15, 2013:
* Minor bug in CW counting is fixed.
July 2, 2013:
version 0.5:
* SAM files can now separately be read into *.depth files, and then merged.
* -nsam parameter to read specific SAM files in the READ mode.
* New CONC mode (--conc) to concatenate/merge different *.depth files using the new -concdepth parameter. These different files may be from different library preparations (see below).
* Multiple library support added.
* Several bug fixes.
November 26, 2012:
version 0.41:
* Bugs in non-autosomal chromosome processing for male samples are fixed.
September 23, 2012:
version 0.4:
* Pseudoautosomal support added through -pseudoa paramater. You can enter the pseudoautosomal regions in BED format in the PREP mode. This is optional; but the configuration file generated and used by this version is not compatible with the previous versions. You need to recreate the configuration file using the PREP mode.
* Code cleanup to facilitate easier addition of new features.
June 1, 2012
version 0.35:
* SAM headers are now ignored.
December 7, 2011
version 0.34:
* Segmentation fault with some kernels & gcc due to an unallocated string is fixed.
October 13, 2011
version 0.33:
* Compilation errors in MacOSX are fixed.
* Compilation error in x86_64 systems with gcc version > 4.33 is fixed.
July 22, 2011
version 0.32:
* Bug in parsing chromosome names that end with whitespace is fixed.
June 22, 2011
version 0.31:
* Bug causing infinite loop in control region selection is fixed.
April 16, 2011
version 0.3:
* Bug in GC normalization fixed
* Bug in CN estimation in chrX and chrY for male mammals is fixed.
March 3, 2011
GC counting bug in LW when an assembly gap is 1 character is fixed. (version 0.22)
March 2, 2011
Bug causing segmentation fault when CW_SIZE is set to a small value is fixed. (version 0.21)
February 25, 2011
A bug in GC normalization is fixed. (version 0.2)
January 23, 2011
SW normalization implemented (copy paste from LW ;-) )
December 27, 2010
LW normalization implemented
December 21, 2010
a bug in handling file names is fixed
December 14, 2010
fixes to control selection: normalization is done AFTER controls are selected
Multiplicative GC scaling option (--multgc)
November 18, 2010
added removing low coverage windows from controls
November 14, 2010
version 0.1-rc
added iteration until min >= mean - 3std ; and 2std for chrX
November 11, 2010
version 0.1-alpha