Mercurial > repos > ryanmorin > nextgen_variant_identification

//v0.12.1-rc1
Added BAM file reading

//v0.11.8
Nov, 2009
Added -M option to read alpha, beta and delta from a space separated text file
	alpha 1 2 3
	beta 1 2 3
	delta 1 2 3

Added alpha, beta and delta command line parameters.

BUGFIX: a variable was not being initialized in readModel() which caused segmentation faults randomly.

//v0.11.7
29 October, 2009
Changed behaviour of SNVmix1 mode to allow map quality filtering, this was previously done at MAQ's pileup
generation which samtools does not support.

-t SNVMix1   will now threshold on -q BASEQ and -Q MAPQ , consider the passing qualities to be perfect.

The default values for -q and -Q were changed to more reasonable levels anything Q19 and below is ignored
unless the user provides -q and -Q values.

//v0.11.5
16 September, 2009
rgoya: changed some type definitions from int to unsigned/signed chars, less memory footprint when training

//v0.11.4
16 September, 2009
rgoya: Added checks and perrors in some malloc that were missing it

//v0.11.3
15 September, 2009
rgoya: Added SNVMix1 functionality with '-t SNVMix1'

//v0.11.2
24 July, 2009
rgoya: Fixed a bug that would crash when encountering undercase 'n' as base call in new pileups

21 July, 2009
// v0.11.1
rgoya: Fixed a bug that would reset qualitiy settings '-Q' and '-q' to zero if they were specified before '-t',
	specifying -t before -Q and -q (as was used when testing) had no adverse effects.

16 July, 2009
// v0.11
rgoya: Modified train (-T) functionality to check for convergence instead of just continuing for max-iter

Output was changed to include coverage
// v0.10
rgoya: Dependency on getline() only for linux, when compiled in MacOSX it uses fgetln()
	Depends on gcc defining either: __linux__ or __APPLE__

June 2009
// v0.8
rgoya: This version of SNVMix2 depends on GNU libraries for function getline(), thus libc >= 4.6.27 is needed.
	This dependency will be fixed in the future.

//
Rodrigo Goya, 2009
rgoya@bcgsc.ca

Sohrab Shah, 2009
sshah@bccrc.ca
author	ryanmorin
date	Wed, 12 Oct 2011 19:50:38 -0400
parents
children