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