BAM Helper Classes

class BamAlignment()

bam/bamAlignment.js

BamAlignment.prototype.isMapped()

bam/bamAlignment.js

BamAlignment.prototype.isPaired()

bam/bamAlignment.js

BamAlignment.prototype.isProperPair()

bam/bamAlignment.js

BamAlignment.prototype.isFirstOfPair()

bam/bamAlignment.js

BamAlignment.prototype.isSecondOfPair()

bam/bamAlignment.js

BamAlignment.prototype.isSecondary()

bam/bamAlignment.js

BamAlignment.prototype.isSupplementary()

bam/bamAlignment.js

BamAlignment.prototype.isFailsVendorQualityCheck()

bam/bamAlignment.js

BamAlignment.prototype.isDuplicate()

bam/bamAlignment.js

BamAlignment.prototype.isMateMapped()

bam/bamAlignment.js

BamAlignment.prototype.isNegativeStrand()

bam/bamAlignment.js

BamAlignment.prototype.isMateNegativeStrand()

bam/bamAlignment.js

BamAlignment.prototype.tags()

bam/bamAlignment.js

BamAlignment.prototype.popupData(genomicLocation)

bam/bamAlignment.js

class BamFilter(options)

bam/bamAlignment.js

BamFilter.prototype.pass(alignment)

bam/bamAlignment.js

class BAMTrack(config)

bam/bamTrack.js

BAMTrack.prototype.getFeatures(chr, bpStart, bpEnd)

bam/bamTrack.js

BAMTrack.prototype.altClick(genomicLocation, referenceFrame, event)

bam/bamTrack.js

BAMTrack.prototype.computePixelHeight(alignmentContainer)

bam/bamTrack.js

BAMTrack.prototype.draw(options)

bam/bamTrack.js

BAMTrack.prototype.paintAxis(ctx, pixelWidth, pixelHeight)

bam/bamTrack.js

BAMTrack.prototype.popupMenuItemList(config)

bam/bamTrack.js

BAMTrack.prototype.popupData(genomicLocation, xOffset, yOffset, referenceFrame)

bam/bamTrack.js

BAMTrack.prototype.popupDataWithConfiguration(config)

bam/bamTrack.js

BAMTrack.prototype.menuItemList(popover)

bam/bamTrack.js

class AlignmentContainer(chr, start, end, samplingWindowSize, samplingDepth, pairsSupported)

bam/alignmentContainer.js

AlignmentContainer.prototype.push(alignment)

bam/alignmentContainer.js

AlignmentContainer.prototype.forEach(callback)

bam/alignmentContainer.js

AlignmentContainer.prototype.finish()

bam/alignmentContainer.js

AlignmentContainer.prototype.contains(chr, start, end)

bam/alignmentContainer.js

AlignmentContainer.prototype.hasDownsampledIntervals()

bam/alignmentContainer.js

CoverageMap.prototype.incCounts(alignment)

bam/alignmentContainer.js

class CoverageMap(chr, start, end, alignments, refSeq)

bam/coverageMap.js

class BamAlignmentRow()

bam/bamAlignmentRow.js

BamAlignmentRow.prototype.findCenterAlignment(bpStart, bpEnd)

bam/bamAlignmentRow.js

BamAlignmentRow.prototype.updateScore(genomicLocation, genomicInterval, sortOption)

bam/bamAlignmentRow.js

BamAlignmentRow.prototype.calculateScore(bpStart, bpEnd, interval, sortOption)

bam/bamAlignmentRow.js

class PairedAlignment(firstAlignment)

bam/pairedAlignment.js

PairedAlignment.prototype.setSecondAlignment(alignment)

bam/pairedAlignment.js

PairedAlignment.prototype.popupData(genomicLocation)

bam/pairedAlignment.js

PairedAlignment.prototype.isPaired()

bam/pairedAlignment.js

PairedAlignment.prototype.firstOfPairStrand()

bam/pairedAlignment.js

class BamIndex(indices, blockMin, blockMax, sequenceIndexMap, tabix)

bam/bamIndex.js

BamIndex.prototype.blocksForRange(refId, min, max)

bam/bamIndex.js

class BGZFile(config)

bam/bgzf.js

BGZFile.prototype.nextBlock()

bam/bgzf.js