Utility class to count the number of observation of each kind of base.
Pileup entry representing a match or mismatch.
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.
The type of read (i.e. Fragment, ReadOne, ReadTwo).
The number of reads examined.
The number of reads that became unmapped due to clipping.
The number of reads with any type of clipping prior to clipping with ClipBam.
The number of reads with any type of clipping after clipping with ClipBam, including reads that became unmapped.
The number of reads with the 5' end clipped.
The number of reads with the 3' end clipped.
The number of reads clipped due to overlapping reads.
The number of aligned bases after clipping.
The number of bases clipped prior to clipping with ClipBam.
The number of bases clipped after clipping with ClipBam, including bases from reads that became unmapped.
The number of bases clipped on the 5' end of the read.
The number of bases clipped on the 3 end of the read.
The number of bases clipped due to overlapping reads.
The base trait for all clipping modes.
Pileup entry representing a deletion.
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 as A>C
.
The read number (0 for fragments, 1 for first of pair, 2 for second of pair).
The position or cycle within the read (1-based).
The total number of bases observed at this position.
The total number of errors or non-reference basecalls observed at this position.
The overall error rate at position.
The rate of A>C
(and T>G
) errors at the position.
The rate of A>G
(and T>C
) errors at the position.
The rate of A>T
(and T>A
) errors at the position.
The rate of C>A
(and G>T
) errors at the position.
The rate of C>G
(and G>C
) errors at the position.
The rate of C>T
(and G>A
) errors at the position.
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.
Pileup entry representing an insertion.
Represents a pileup of reads/bases at a single genomic location.
Class that provides methods to build and filter Pileups.
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.
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.
The name of the sample within the pool being reported on.
How many sites were examined at which the reported sample is known to be variant.
How many of the variant sites were sites at which only this sample was variant.
The estimated fraction of the pool that comes from this sample.
The standard error of the estimated fraction.
The lower bound of the 99% confidence interval for the estimated fraction.
The upper bound of the 99% confidence interval for the estimated fraction.
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:
Class that represents all reads from a template within a BAM file.
Updates one or more read groups.
Updates one or more read groups.
Utility methods for working with BAMs.
An enumeration representing the various ways to clip bases within a read.
Holds types and constants related to SamRecord clipping.