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Created with Raphaël 2.2.015Mar141311109875432129Feb262524232221181716151211109875432129Jan28272625232221201918171514121110865430Dec2928262524232221181716merge from developMerge branch 'fix-small_fixes' into 'develop' Merge branch 'feature-general-refactor-biopet' into 'develop' Fixed compile issueMerge remote-tracking branch 'remotes/origin/develop' into feature-general-refactor-biopetGeneral refactor BiopetFix free varsFix typoAdded some release notesMerge branch 'develop' into feature-cnvpipelineMerge branch 'fix-flexiprep-fastqc_report_kmer' into 'develop' Name changingAdded and remove tools from executableMerge branch 'fix-small_fixes' into 'develop' Merge branch 'feature-shiva-docs' into 'develop' Simplify the file check (not on md5)Merge branch 'fix-bowtie2-indexfiles' into 'develop' add amplicon bed file documentationFix: Show a message for those plot, which were not created by FastQC. Some statistics cannot be collected by FastQC such as Kmer when the sequences are clean.Fixed unit testsRemove unused varFix bug when bowtie2 is not able to find reference files ending with .bt2l (new large file definition)Fixed value typeRaise default resourcesRaise default memory for VEPStyle fixesRemove commentAdded piping to freebayesAdding options to freebayesAdded output file to vepMerge branch 'fix-compile_issues' into 'develop' Fixed styleFixed compile issueMerge branch 'feature-small_rna' into 'develop' Merge with changes from developMerge branch 'fix-seqstat-arraysize' into 'develop' Style changeStyle changeMerge branch 'feature-Carp-docs-0.6.0' into 'develop' Fix typo