Releases

2013-09-04: mrCaNaVaR version 0.51 release:

• Minor bug in CW counting is fixed.

2013-07-02: mrCaNaVaR version 0.5 release:

• SAM files can now separately be read into *.depth files, and then merged.
• New -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.

2012-11-26: mrCaNaVaR version 0.41 release:

• Bugs in non-autosomal chromosome processing for male samples are fixed.

2012-09-23: mrCaNaVaR version 0.4 release:

• 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.

2012-06-01: mrCaNaVaR version 0.35 release:

• SAM headers are now ignored.

2011-12-07: mrCaNaVaR version 0.34 release:

• Segmentation fault with some kernels & gcc due to an unallocated string is fixed.

2011-10-17: mrCaNaVaR version 0.33 release:

• Compilation errors in MacOSX are fixed.
• Compilation error in x86_64 systems with gcc version > 4.33 is fixed.

2011-08-15: mrCaNaVaR version 0.32 release:

• Minor bug in parsing chromosome names that end with whitespace is fixed.

2011-06-22: mrCaNaVaR version 0.31 release:

• Bug causing infinite loop in control region selection is fixed..

2011-04-16: mrCaNaVaR version 0.3 release:

• Bug in GC normalization is fixed.
• Bug in CN estimation in chrX and chrY for male mammals is fixed.

2011-03-04: mrCaNaVaR version 0.22 release:

• GC counting bug in LW when an assembly gap is 1 character is fixed.

2011-03-02: mrCaNaVaR version 0.21 release:

• Bug causing segmentation fault when CW_SIZE is set to a small value is fixed.

2011-02-25: mrCaNaVaR version 0.2 release:

• A bug in GC normalization is fixed.

2011-01-28: mrCaNaVaR version 0.1 release:

• Initial release of mrCaNaVaR.
• This version only predicts absolute copy numbers. CNV interval output will be included in the next release. For the time being, you can select intervals with increased copy number (i.e. > 2.5) and merge such intervals using BEDtools.