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broad.pda.seq.alignment.AlignmentUtils Member List

This is the complete list of members for broad.pda.seq.alignment.AlignmentUtils, including all inherited members.

getSizesFromSAM(String samFileName)broad.pda.seq.alignment.AlignmentUtilsstatic
loadAlignmentData(String alignmentFile)broad.pda.seq.alignment.AlignmentUtilsstatic
loadAlignmentData(String alignmentFile, boolean loadChromosomeStats)broad.pda.seq.alignment.AlignmentUtilsstatic
loadAlignmentData(String alignmentFile, boolean loadChromosomeStats, int minMappingQuality)broad.pda.seq.alignment.AlignmentUtilsstatic
loadAlignmentData(String alignmentFile, boolean loadChromosomeStats, int minMappingQuality, boolean removeDuplicateFlags)broad.pda.seq.alignment.AlignmentUtilsstatic
loadAlignmentData(String alignmentFile, boolean loadChromosomeStats, boolean removeDuplicateFlags, boolean weighReadCounts)broad.pda.seq.alignment.AlignmentUtilsstatic
loadAlignmentData(String alignmentFile, boolean loadChromosomeStats, int minMappingQuality, boolean removeDuplicateFlags, boolean weighReadCounts)broad.pda.seq.alignment.AlignmentUtilsstatic
loadAlignmentData(String alignmentFile, boolean loadChromosomeStats, int minMappingQuality, boolean removeDuplicateFlags, boolean weighReadCounts, String strand)broad.pda.seq.alignment.AlignmentUtilsstatic
loadAlignmentData(String alignmentFile, boolean loadChromosomeStats, int minMappingQuality, boolean removeDuplicateFlags, boolean weighReadCounts, String strand, boolean loadPairsAsFragments)broad.pda.seq.alignment.AlignmentUtilsstatic
main(String[] args)broad.pda.seq.alignment.AlignmentUtilsstatic
SAMFormatFullBED(SAMRecord sam)broad.pda.seq.alignment.AlignmentUtilsstatic
scoreAnnotations(BEDReader annotationReader, ContinuousDataAlignmentModel data)broad.pda.seq.alignment.AlignmentUtilsstatic
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