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. Designed to be used to filter out reads that might confuse variant callers and lead to false positive variant calls.
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Instance Constructors
- new FilterBam(input: commons.CommonsDef.PathToBam, output: commons.CommonsDef.PathToBam, intervals: Option[commons.CommonsDef.PathToIntervals] = None, removeDuplicates: Boolean = true, removeUnmappedReads: Boolean = true, minMapQ: Int = 1, removeSingleEndMappings: Boolean = false, removeSecondaryAlignments: Boolean = true, minInsertSize: Option[Int] = None, maxInsertSize: Option[Int] = None, minMappedBases: Option[Int] = None)
Value Members
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final
def
!=(arg0: Any): Boolean
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final
def
##(): Int
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- def +(other: String): String
- def ->[B](y: B): (FilterBam, B)
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final
def
==(arg0: Any): Boolean
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final
def
asInstanceOf[T0]: T0
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def
buildInputIterator(in: SamSource, intervalListFile: Option[Path]): Iterator[SamRecord]
If intervalListFile is null return an interator over all the input, otherwise returns an iterator over only those reads that overlap one or more of the intervals in the file.
If intervalListFile is null return an interator over all the input, otherwise returns an iterator over only those reads that overlap one or more of the intervals in the file.
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def
clone(): AnyRef
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- @throws( ... )
- def ensuring(cond: (FilterBam) ⇒ Boolean, msg: ⇒ Any): FilterBam
- def ensuring(cond: (FilterBam) ⇒ Boolean): FilterBam
- def ensuring(cond: Boolean, msg: ⇒ Any): FilterBam
- def ensuring(cond: Boolean): FilterBam
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final
def
eq(arg0: AnyRef): Boolean
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def
equals(arg0: Any): Boolean
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def
fail(exit: Int, message: String): Nothing
Fail with a specific error code and message.
Fail with a specific error code and message.
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- FgBioTool
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def
fail(message: String): Nothing
Fail with the default exit code and a message.
Fail with the default exit code and a message.
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- FgBioTool
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def
fail(exit: Int): Nothing
Fail with just an exit code.
Fail with just an exit code.
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def
finalize(): Unit
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- def formatted(fmtstr: String): String
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final
def
getClass(): Class[_]
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def
hashCode(): Int
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- val input: commons.CommonsDef.PathToBam
- val intervals: Option[commons.CommonsDef.PathToIntervals]
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def
invalid(message: String): Nothing
Generates a new validation exception with the given message.
Generates a new validation exception with the given message.
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- FgBioTool
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final
def
isInstanceOf[T0]: Boolean
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lazy val
logger: Logger
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- val maxInsertSize: Option[Int]
- val minInsertSize: Option[Int]
- val minMapQ: Int
- val minMappedBases: Option[Int]
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final
def
ne(arg0: AnyRef): Boolean
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final
def
notify(): Unit
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final
def
notifyAll(): Unit
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- val output: commons.CommonsDef.PathToBam
- val removeDuplicates: Boolean
- val removeSecondaryAlignments: Boolean
- val removeSingleEndMappings: Boolean
- val removeUnmappedReads: Boolean
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final
def
synchronized[T0](arg0: ⇒ T0): T0
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def
toString(): String
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def
validate(test: Boolean, message: ⇒ String): Unit
Generates a validation exception if the test value is false.
Generates a validation exception if the test value is false.
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- FgBioTool
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final
def
wait(): Unit
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def
wait(arg0: Long, arg1: Int): Unit
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final
def
wait(arg0: Long): Unit
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- def →[B](y: B): (FilterBam, B)