Index

C

checkBlackListGene() (in module iCallSV.filterAnnotatedSV) checkDellyAnalysisType() (in module iCallSV.checkparameters) checkDir() (in module iCallSV.checkparameters) checkEmpty() (in module iCallSV.checkparameters) checkEventInIntronFlag() (in module iCallSV.filterAnnotatedSV) checkFile() (in module iCallSV.checkparameters)

checkGeneListToKeep() (in module iCallSV.filterAnnotatedSV) CheckIfItIsBlacklisted() (in module iCallSV.checkBlackList) CheckIfItIsHotspot() (in module iCallSV.checkHotSpotList) checkInt() (in module iCallSV.checkparameters) Convert2targetSeqView() (in module iCallSV.dellyVcf2targetSeqView)

G

GetCaseFlag() (in module iCallSV.FilterDellyCalls) GetControlFlag() (in module iCallSV.FilterDellyCalls)

GetFilteredRecords() (in module iCallSV.FilterDellyCalls)

I

iCallSV (module) iCallSV.checkBlackList (module) iCallSV.checkHotSpotList (module) iCallSV.checkparameters (module) iCallSV.combineVCF (module) iCallSV.dellyVcf2Tab (module) iCallSV.dellyVcf2targetSeqView (module) iCallSV.filterAnnotatedSV (module) iCallSV.FilterDellyCalls (module) iCallSV.iCallSV (module) iCallSV.launch_FilterDellyCalls (module)

iCallSV.launch_Run_Delly (module) iCallSV.launchThreads (module) iCallSV.make_analysis_dir (module) iCallSV.makebamindex (module) iCallSV.mergeFinalFiles (module) iCallSV.Run_Delly (module) iCallSV.Run_iAnnotateSV (module) iCallSV.Run_samblaster (module) iCallSV.Run_targetSeqView (module) iCallSV.sortbamByCoordinate (module) iCallSV.sortbamByReadName (module)

L

launch_delly_for_different_analysis_type() (in module iCallSV.launch_Run_Delly)

launch_filterdellycalls_for_different_analysis_type() (in module iCallSV.launch_FilterDellyCalls)

M

MakeIndex() (in module iCallSV.makebamindex) makeOutputDir() (in module iCallSV.make_analysis_dir)

myThread (class in iCallSV.launchThreads)

P

print_time() (in module iCallSV.launchThreads)

R

ReadBlackListFile() (in module iCallSV.checkBlackList) ReadHotSpotFile() (in module iCallSV.checkHotSpotList)

run() (iCallSV.launchThreads.myThread method) (in module iCallSV.FilterDellyCalls) (in module iCallSV.Run_Delly) (in module iCallSV.Run_iAnnotateSV) (in module iCallSV.Run_samblaster) (in module iCallSV.Run_targetSeqView) (in module iCallSV.combineVCF) (in module iCallSV.filterAnnotatedSV) (in module iCallSV.mergeFinalFiles)

S

sortBam() (in module iCallSV.sortbamByCoordinate) (in module iCallSV.sortbamByReadName)

V

vcf2tab() (in module iCallSV.dellyVcf2Tab)