| Package | Description |
|---|---|
| picard.sam | |
| picard.sam.markduplicates.util |
| Class and Description |
|---|
| AbstractAlignmentMerger
Abstract class that coordinates the general task of taking in a set of alignment information,
possibly in SAM format, possibly in other formats, and merging that with the set of all reads
for which alignment was attempted, stored in an unmapped SAM file.
|
| FilterSamReads.Filter |
| PrimaryAlignmentSelectionStrategy
Given a set of alignments for a read or read pair, mark one alignment as primary, according to whatever
strategy is appropriate.
|
| RevertOriginalBaseQualitiesAndAddMateCigar.CanSkipSamFile
Used as a return for the canSkipSAMFile function.
|
| ValidateSamFile.Mode |
| ViewSam.AlignmentStatus |
| ViewSam.PfStatus |
| Class and Description |
|---|
| DuplicationMetrics
Metrics that are calculated during the process of marking duplicates
within a stream of SAMRecords.
|