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Created with Raphaël 2.2.027Mar26252423201918171615141312111098765432127Feb26242319181716151413Merge branch 'develop' into feature-vcfwithvcfChange filenames to proper camelCaseChange variables to proper camelCaseMerge branch 'feature-VcfWithVcf_peter' into 'feature-vcfwithvcf'Added note on cufflinks traitSwitch to scala 2.10Merge branch 'feature-auto_memory' into 'develop'change var namefixed varProperly open and close files in ExtractAlignedFastqfixed typoTweaking setting after testingFix error in ExtractAlignedFastq single-end mode where the input file is rewrittenMerge branch 'feature-gentrap_docs' into 'develop'Merge branch 'patch-versioning' into 'develop'Update docs in main Gentrap pipelineAdded logger message on retryUpdate main help messageUpdate dirty warning messageUse FullVersion throughoutUse package version in GentrapAdd nl.lumc.sasc.biopet package object to store package-wide informationAdding removal of old vmem tag from resourcesSwitch gatk parts to new memory limitsAdded a retry methodChange limits to coreMemoryRemove method to set memlimitChanged memory limit aproachAdded some errors when there is a field conflictChange setup so it can presume vcf types instead of forcing it to strings. Some style changes. Added support for different inputField and outputFieldFix wrong output setting in CustomVarScanSet idsorting job as intermediateMerge branch 'hotfix-v0.3.1'v0.3.1v0.3.1Bump version from 0.3.0 to 0.3.1Also change dependency for cutadeptFix dependency bug in flexiprepFix incorrectly passed java flags for piped VarScan commandMerge branch 'feature-vcfstats' into 'develop'Fix variable and add more docsMerge branch 'patch-varscan' into 'develop'