package bam
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Type Members
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class
AutoGenerateReadGroupsByName extends FgBioTool with LazyLogging
- Annotations
- @ClpAnnotation()
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case class
BaseCounts(a: Int, c: Int, g: Int, t: Int, n: Int) extends Product with Serializable
Utility class to count the number of observation of each kind of base.
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case class
BaseEntry(rec: SamRecord, offset: Int) extends PileupEntry with Product with Serializable
Pileup entry representing a match or mismatch.
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class
ClipBam extends FgBioTool with LazyLogging
- Annotations
- @ClpAnnotation()
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case class
ClippingMetrics(read_type: ReadType, reads: Long = 0, reads_unmapped: Long = 0, reads_clipped_pre: Long = 0, reads_clipped_post: Long = 0, reads_clipped_five_prime: Long = 0, reads_clipped_three_prime: Long = 0, reads_clipped_overlapping: Long = 0, bases: Long = 0, bases_clipped_pre: Long = 0, bases_clipped_post: Long = 0, bases_clipped_five_prime: Long = 0, bases_clipped_three_prime: Long = 0, bases_clipped_overlapping: Long = 0) extends Metric with Product with Serializable
Metrics produced by ClipBam that detail how many reads and bases are clipped respectively.
Metrics produced by ClipBam that detail how many reads and bases are clipped respectively.
- read_type
The type of read (i.e. Fragment, ReadOne, ReadTwo).
- reads
The number of reads examined.
- reads_unmapped
The number of reads that became unmapped due to clipping.
- reads_clipped_pre
The number of reads with any type of clipping prior to clipping with ClipBam.
- reads_clipped_post
The number of reads with any type of clipping after clipping with ClipBam, including reads that became unmapped.
- reads_clipped_five_prime
The number of reads with the 5' end clipped.
- reads_clipped_three_prime
The number of reads with the 3' end clipped.
- reads_clipped_overlapping
The number of reads clipped due to overlapping reads.
- bases
The number of aligned bases after clipping.
- bases_clipped_pre
The number of bases clipped prior to clipping with ClipBam.
- bases_clipped_post
The number of bases clipped after clipping with ClipBam, including bases from reads that became unmapped.
- bases_clipped_five_prime
The number of bases clipped on the 5' end of the read.
- bases_clipped_three_prime
The number of bases clipped on the 3 end of the read.
- bases_clipped_overlapping
The number of bases clipped due to overlapping reads.
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sealed
trait
ClippingMode extends EnumEntry
The base trait for all clipping modes.
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case class
DeletionEntry(rec: SamRecord, offset: Int) extends PileupEntry with Product with Serializable
Pileup entry representing a deletion.
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class
ErrorRateByReadPosition extends FgBioTool with LazyLogging
- Annotations
- @ClpAnnotation()
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case class
ErrorRateByReadPositionMetric(read_number: Int, position: Int, bases_total: Count, errors: Count, error_rate: Double, a_to_c_error_rate: Double, a_to_g_error_rate: Double, a_to_t_error_rate: Double, c_to_a_error_rate: Double, c_to_g_error_rate: Double, c_to_t_error_rate: Double) extends Metric with Product with Serializable
Metrics produced by
ErrorRateByReadPosition
describing the number of base observations and substitution errors at each position within each sequencing read.Metrics produced by
ErrorRateByReadPosition
describing the number of base observations and substitution errors at each position within each sequencing read. Error rates are given for the overall substitution error rate and also for each kind of substitution separately. Instead of reporting 12 substitution rates, 6 are reported where complementary substitutions are grouped together, e.g.T>G
substitutions are reported asA>C
.- read_number
The read number (0 for fragments, 1 for first of pair, 2 for second of pair).
- position
The position or cycle within the read (1-based).
- bases_total
The total number of bases observed at this position.
- errors
The total number of errors or non-reference basecalls observed at this position.
- error_rate
The overall error rate at position.
- a_to_c_error_rate
The rate of
A>C
(andT>G
) errors at the position.- a_to_g_error_rate
The rate of
A>G
(andT>C
) errors at the position.- a_to_t_error_rate
The rate of
A>T
(andT>A
) errors at the position.- c_to_a_error_rate
The rate of
C>A
(andG>T
) errors at the position.- c_to_g_error_rate
The rate of
C>G
(andG>C
) errors at the position.- c_to_t_error_rate
The rate of
C>T
(andG>A
) errors at the position.
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class
EstimatePoolingFractions extends FgBioTool with LazyLogging
- Annotations
- @ClpAnnotation()
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class
FilterBam extends FgBioTool with LazyLogging
Program which takes in a BAM file and filters out all reads for templates that match one or more criteria.
Program which takes in a BAM file and filters out all reads for templates that match one or more criteria. Designed to be used to filter out reads that might confuse variant callers and lead to false positive variant calls.
- Annotations
- @ClpAnnotation()
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class
FindSwitchbackReads extends FgBioTool with LazyLogging
- Annotations
- @ClpAnnotation()
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class
FindTechnicalReads extends FgBioTool with LazyLogging
- Annotations
- @ClpAnnotation()
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case class
InsertionEntry(rec: SamRecord, offset: Int) extends PileupEntry with Product with Serializable
Pileup entry representing an insertion.
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case class
Pileup[A <: PileupEntry](refName: String, refIndex: Int, pos: Int, pile: Seq[A]) extends Iterable[A] with Product with Serializable
Represents a pileup of reads/bases at a single genomic location.
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class
PileupBuilder extends AnyRef
Class that provides methods to build and filter Pileups.
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sealed
trait
PileupEntry extends AnyRef
Base trait for pileup entries that exposes the com.fulcrumgenomics.bam.api.SamRecord and the 0-based offset into the record's bases and qualities that is relevant to the pileup.
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case class
PoolingFractionMetric(sample: String, variant_sites: Count, singletons: Count, estimated_fraction: Proportion, standard_error: Double, ci99_low: Proportion, ci99_high: Proportion) extends Metric with Product with Serializable
Metrics produced by
EstimatePoolingFractions
to quantify the estimated proportion of a sample mixture that is attributable to a specific sample with a known set of genotypes.Metrics produced by
EstimatePoolingFractions
to quantify the estimated proportion of a sample mixture that is attributable to a specific sample with a known set of genotypes.- sample
The name of the sample within the pool being reported on.
- variant_sites
How many sites were examined at which the reported sample is known to be variant.
- singletons
How many of the variant sites were sites at which only this sample was variant.
- estimated_fraction
The estimated fraction of the pool that comes from this sample.
- standard_error
The standard error of the estimated fraction.
- ci99_low
The lower bound of the 99% confidence interval for the estimated fraction.
- ci99_high
The upper bound of the 99% confidence interval for the estimated fraction.
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class
RandomizeBam extends FgBioTool with LazyLogging
- Annotations
- @ClpAnnotation()
- sealed trait ReadType extends EnumEntry
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class
RemoveSamTags extends FgBioTool
- Annotations
- @ClpAnnotation()
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class
SamRecordClipper extends AnyRef
Provides a suite of methods for clipping (soft- and hard-) bases from the beginnings and ends of reads in various ways.
Provides a suite of methods for clipping (soft- and hard-) bases from the beginnings and ends of reads in various ways. Cigar strings, bases, qualities and alignment positions are all correctly adjusted post-clipping.
Note that there are several "flavours" of method:
- Ones that work on the start and end of the read in whatever orientation the read is in, vs. working on the 5' or 3' end of the read
- Ones that attempt to clip an additional N bases beyond any clipping already provided (clip[Start|End|5PrimeEnd|3PrimeEnd]OfAlignment) and ones that attempt to make it so that the read has N bases clipped, including any existing clipping (clip[Start|End|5PrimeEnd|3PrimeEnd]OfRead)
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class
SetMateInformation extends FgBioTool with LazyLogging
- Annotations
- @ClpAnnotation()
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class
SortBam extends FgBioTool with LazyLogging
- Annotations
- @ClpAnnotation()
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class
SplitBam extends FgBioTool with LazyLogging
- Annotations
- @ClpAnnotation()
- sealed trait SplitType extends EnumEntry
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case class
Template(r1: Option[SamRecord], r2: Option[SamRecord], r1Supplementals: Seq[SamRecord] = Nil, r2Supplementals: Seq[SamRecord] = Nil, r1Secondaries: Seq[SamRecord] = Nil, r2Secondaries: Seq[SamRecord] = Nil) extends Product with Serializable
Class that represents all reads from a template within a BAM file.
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class
TrimPrimers extends FgBioTool with LazyLogging
- Annotations
- @ClpAnnotation()
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class
UpdateReadGroups extends FgBioTool with LazyLogging
Updates one or more read groups.
Updates one or more read groups.
- Annotations
- @ClpAnnotation()
Value Members
-
object
Bams extends LazyLogging
Utility methods for working with BAMs.
- object BaseCounts extends Serializable
-
object
ClippingMode extends FgBioEnum[ClippingMode]
An enumeration representing the various ways to clip bases within a read.
- object ErrorRateByReadPositionMetric extends Serializable
- object FindSwitchbackReads
- object ReadType extends FgBioEnum[ReadType]
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object
SamRecordClipper
Holds types and constants related to SamRecord clipping.
- object SplitType extends FgBioEnum[SplitType]
- object Template extends Serializable
- object TrimPrimers