Applying this algorithm iteratively can be done from outside if given some intermediate results. Thus, the loop should be eliminated and opportunities given to access the intermediate results.
What needs to be done?
[x] adjust algorithmic structure as sketched below (issue #47)
[x] make sequential output (issue #45)
[x] add opportunity to output of the candidate set of reads (issue #41)
[x] add opportunity to make use of user-input masks (and reads) (issue #48)
Sketch of algorithmic structure
// Initialization
maskBadRegions()
filterReadAlignments()
// Close Gaps
buildPileUps()
for each pileUp do
selectGoodReads()
cropAndValidateReads()
buildConsensus()
// Finish
pruneOverfilledGaps()
generateOutput()
Applying this algorithm iteratively can be done from outside if given some intermediate results. Thus, the loop should be eliminated and opportunities given to access the intermediate results.
What needs to be done?
Sketch of algorithmic structure