- m -

• MAIN_ARRAY_LEFT : broad.pda.seq.rap.CountProbes
• MAIN_ARRAY_RIGHT : broad.pda.seq.rap.CountProbes
• MASK_FILE : broad.pda.seq.rap.GenomeCommandLineProgram
• match : umms.core.annotation.PSLRecord
• MATCH_OPPOSITE_STRAND : broad.pda.seq.rap.DistanceToBED
• mateCigarFlag : umms.core.writers.PairedEndWriter
• mateLineFlag : umms.core.writers.PairedEndWriter
• mateSequenceFlag : umms.core.writers.PairedEndWriter
• MAX_DISTANCE : umms.core.annotation.AbstractAnnotation
• MAX_FRAGMENT_LENGTH : broad.pda.seq.rap.GenomeCommandLineProgram
• MAX_INSERT : broad.pda.samtools.PairedEndTDF , broad.pda.samtools.SAMPairedEndFileReader
• maxDist : broad.pda.differentialExpression.FWERDistribution
• maxFragmentLengthData : broad.pda.seq.clip.SampleData , broad.pda.seq.protection.SampleData
• maxFragmentLengthGeneScores : broad.pda.seq.clip.SampleData
• METRICS : broad.pda.samtools.FilterPairedReadsByMAQ
• MIDDLE_LENGTH : broad.pda.seq.rap.PlotAggregateRegions
• MIN_MAPPING_QUALITY : broad.pda.seq.rap.GenomeCommandLineProgram
• MIN_WINDOW_COUNT : broad.pda.seq.protection.TwoSampleScanSkellamPeakCaller
• minDist : broad.pda.differentialExpression.FWERDistribution
• MINIMUM_MAPPING_QUALITY : broad.pda.samtools.FilterPairedReadsByMAQ
• MISMATCH : jaligner.Markups
• MmeI : broad.core.primer3.RestrictionEnzyme
• MRNA_ARRAY_LEFT : broad.pda.seq.rap.CountProbes
• MRNA_ARRAY_RIGHT : broad.pda.seq.rap.CountProbes