org.hammerlab.genomics.readsets.io
if set, include only mapped reads that overlap the given loci
include only reads that do not have the duplicate bit set
include only reads that do not have the failedVendorQualityChecks bit set
include only reads are paired-end reads
Minimum Phred-scaled alignment score for a read
Maximum on-disk size to allow Hadoop splits to be; useful to set below the on-disk block-size for BAMs where the reads compress extra-well, resulting in unwieldy numbers of reads per fixed-disk-size partition.
include only reads are paired-end reads
Maximum on-disk size to allow Hadoop splits to be; useful to set below the on-disk block-size for BAMs where the reads compress extra-well, resulting in unwieldy numbers of reads per fixed-disk-size partition.
Minimum Phred-scaled alignment score for a read
include only reads that do not have the duplicate bit set
if set, include only mapped reads that overlap the given loci
include only reads that do not have the failedVendorQualityChecks bit set
Configuring how/which reads are loaded can be an important optimization.
Most of these fields are commonly used filters. For boolean fields, setting a field to true will result in filtering on that field. The result is the intersection of the filters (i.e. reads must satisfy ALL filters).
if set, include only mapped reads that overlap the given loci
include only reads that do not have the duplicate bit set
include only reads that do not have the failedVendorQualityChecks bit set
include only reads are paired-end reads
Minimum Phred-scaled alignment score for a read
Maximum on-disk size to allow Hadoop splits to be; useful to set below the on-disk block-size for BAMs where the reads compress extra-well, resulting in unwieldy numbers of reads per fixed-disk-size partition.