AddOrReplaceReadGroup returns a filter for adding or replacing the read group both in the Header and in each Alignment.

AddPGLine returns a filter for adding a @PG tag to a Header, and ensuring that it is the first one in the chain.

AddREFID is a filter for adding the refid (index in the reference sequence dictionary) to alignments as temporary values.

CleanSam is a filter for soft-clipping an alignment at the end of a reference sequence, and setting MAPQ to 0 if unmapped.

KeepOptionalFields returns a filter for removing all but a list of given optional fields in an alignment.

LoadAndCombineBQSRTables loads and merges multiple recalibration tables from file into a single, new recalibration table.

LoadAndCombineDuplicateMetrics loads partial duplication metrics from file and combines them.

MarkDuplicates returns a filter for marking duplicate alignments.

MarkOpticalDuplicates implements a function for calculating duplication metrics for a set of reads, optical pixel distance = 100.

MarkOpticalDuplicatesWithPixelDistance implements a function for calculating duplication metrics for a set of reads.

NewBaseRecalibrator returns a struct for the first step of base recalibration.

NewBaseRecalibratorTables returns a struct for storing the result of the base recalibration.

PrintDuplicatesMetrics writes the duplication metrics for a set of reads to a file.

PrintDuplicatesMetricsToIntermediateFile writes the duplicate metrics to a gob file.

RemoveDuplicateReads is a filter for removing duplicate sam-alignment instances, based on FLAG.

RemoveMappingQualityLessThan is a filter for removing reads that do not match or exceed the given mapping quality.

RemoveNonExactMappingReads is a filter that removes all reads that are not exact matches with the reference (soft-clipping ok), based on CIGAR string (only M and S allowed).

RemoveNonExactMappingReadsStrict is a filter that removes all reads that are not exact matches with the reference, based on the optional fields X0=1 (unique mapping), X1=0 (no suboptimal hit), XM=0 (no mismatch), XO=0 (no gap opening), XG=0 (no gap extension).

RemoveNonOverlappingReads returns a filter for removing all reads that do not overlap with a set of regions specified by a bed file.

RemoveOptionalFields returns a filter for removing optional fields in an alignment.

RemoveOptionalReads is a filter for removing alignments that represent optional information in elPrep.

RemoveUnmappedReads is a filter for removing unmapped sam-alignment instances, based on FLAG.

RemoveUnmappedReadsStrict is a filter for removing unmapped sam-alignment instances, based on FLAG, or POS=0, or RNAME=*.

RenameChromosomes is a filter for prepending "chr" to the reference sequence names in a Header, and in RNAME and RNEXT in each Alignment.

ReplaceReferenceSequenceDictionary returns a filter for replacing the reference sequence dictionary in a Header.

ReplaceReferenceSequenceDictionaryFromSamFile returns a filter for replacing the reference sequence dictionary in a Header with one parsed from the given SAM/DICT file.

Symbols for optional fields used for determining exact matches.

Symbols for optional fields used for determining exact matches.

Symbols for optional fields used for determining exact matches.

Symbols for optional fields used for determining exact matches.

Symbols for optional fields used for determining exact matches.

BaseRecalibrator implements the first step of base recalibration.

BaseRecalibratorTables is the result of the base recalibration.

DuplicatesCountHistograms keeps tracks of metrics for the number of pcr vs optical duplicates per list of duplicates.

DuplicatesCtr implements a struct that stores metrics about reads such as the number of (optical) duplicates, unmapped reads, etc.

DuplicatesCtrMap maps library names to duplicate counters.