Mercurial > repos > ryanmorin > nextgen_variant_identification
comparison SNV/SNVMix2_source/SNVMix2-v0.12.1-rc1/CHANGELOG @ 0:74f5ea818cea
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| author | ryanmorin |
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| date | Wed, 12 Oct 2011 19:50:38 -0400 |
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| -1:000000000000 | 0:74f5ea818cea |
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| 1 //v0.12.1-rc1 | |
| 2 Added BAM file reading | |
| 3 | |
| 4 //v0.11.8 | |
| 5 Nov, 2009 | |
| 6 Added -M option to read alpha, beta and delta from a space separated text file | |
| 7 alpha 1 2 3 | |
| 8 beta 1 2 3 | |
| 9 delta 1 2 3 | |
| 10 | |
| 11 Added alpha, beta and delta command line parameters. | |
| 12 | |
| 13 BUGFIX: a variable was not being initialized in readModel() which caused segmentation faults randomly. | |
| 14 | |
| 15 //v0.11.7 | |
| 16 29 October, 2009 | |
| 17 Changed behaviour of SNVmix1 mode to allow map quality filtering, this was previously done at MAQ's pileup | |
| 18 generation which samtools does not support. | |
| 19 | |
| 20 -t SNVMix1 will now threshold on -q BASEQ and -Q MAPQ , consider the passing qualities to be perfect. | |
| 21 | |
| 22 The default values for -q and -Q were changed to more reasonable levels anything Q19 and below is ignored | |
| 23 unless the user provides -q and -Q values. | |
| 24 | |
| 25 //v0.11.5 | |
| 26 16 September, 2009 | |
| 27 rgoya: changed some type definitions from int to unsigned/signed chars, less memory footprint when training | |
| 28 | |
| 29 //v0.11.4 | |
| 30 16 September, 2009 | |
| 31 rgoya: Added checks and perrors in some malloc that were missing it | |
| 32 | |
| 33 //v0.11.3 | |
| 34 15 September, 2009 | |
| 35 rgoya: Added SNVMix1 functionality with '-t SNVMix1' | |
| 36 | |
| 37 //v0.11.2 | |
| 38 24 July, 2009 | |
| 39 rgoya: Fixed a bug that would crash when encountering undercase 'n' as base call in new pileups | |
| 40 | |
| 41 21 July, 2009 | |
| 42 // v0.11.1 | |
| 43 rgoya: Fixed a bug that would reset qualitiy settings '-Q' and '-q' to zero if they were specified before '-t', | |
| 44 specifying -t before -Q and -q (as was used when testing) had no adverse effects. | |
| 45 | |
| 46 16 July, 2009 | |
| 47 // v0.11 | |
| 48 rgoya: Modified train (-T) functionality to check for convergence instead of just continuing for max-iter | |
| 49 | |
| 50 Output was changed to include coverage | |
| 51 // v0.10 | |
| 52 rgoya: Dependency on getline() only for linux, when compiled in MacOSX it uses fgetln() | |
| 53 Depends on gcc defining either: __linux__ or __APPLE__ | |
| 54 | |
| 55 June 2009 | |
| 56 // v0.8 | |
| 57 rgoya: This version of SNVMix2 depends on GNU libraries for function getline(), thus libc >= 4.6.27 is needed. | |
| 58 This dependency will be fixed in the future. | |
| 59 | |
| 60 // | |
| 61 Rodrigo Goya, 2009 | |
| 62 rgoya@bcgsc.ca | |
| 63 | |
| 64 Sohrab Shah, 2009 | |
| 65 sshah@bccrc.ca |