Index

A

alignment module

C

calling module checkTools() (in module software)

config module cropping module

D

detectFilesToCrop() (in module cropping) discardHighError() (in module quality) downloads module

downloadSRAs() (in module downloads) downloadTools() (in module software)

E

execCmd() (in module util)

extractUnaligned() (in module alignment)

F

filterAS_StrandOddsRatio() (in module calling)

G

generateGraphs() (in module results)

getExperimentsList() (in module downloads)

L

loadConfig() (in module config) (in module logger)

logger module

M

makeDirectory() (in module util) mergeCalling() (in module results) module alignment calling config cropping downloads logger quality results software util

Q

quality module

R

results module runBWA() (in module alignment) runCommand() (in module util) runFastQC() (in module quality) runGMAP() (in module alignment) runHisat2() (in module alignment) runJacusa() (in module calling)

runMagicBlast() (in module alignment) runMinimap2() (in module alignment) runQualimap() (in module quality) runReditools2() (in module calling) runSlurm() (in module util) runSnpEff() (in module results) runSTAR() (in module alignment) runTrimGalore() (in module cropping) runTrimmomatic() (in module cropping)

S

setWorkPath() (in module config) software module

sortAlignments() (in module alignment) stopProgram() (in module util)

U

util module

W

waitForJobs() (in module util)