SAM

gngs.SAM

```
class SAM
extends java.lang.Object
```
Adds various Groovy idioms and convenience features to the Picard SamReader.
There are three major classes of functionality supported:
Iterating through and filtering reads in various ways
Generating pileups and calculating read depth / coverage
Accessing meta data (read groups, sample information, etc)

For simple looping, the eachRead(Closure) static method can be used without creating a SAM object at all:

 SAM.eachRead { SAMRecord r -> println r.readName }

 new SAM("test.bam").eachPair { r1, r2 -> assert r1.readName == r2.readName }

A region can be optionally passed to iterate over:

 new SAM("test.bam").eachPair("chr1",1000,2000) { r1, r2 -> assert r1.readName == r2.readName }

new SAM("test.bam").filter("out.bam") { it.mappingQuality > 30 }

 new SAM("test.bam").pileup("chr1",1000,2000) { p -> 
     println "There are ${p.countOf('A')} A bases at position chr1:$p.position" 
 }

Pileup

Notes:

Most operations filter out reads with mapping quality 0 by default. To avoid this, set the minMappingQuality property on the SAM object.
All operations with this class require the BAM file to be indexed.
SAM and BAM files are treated transparently the same.

Progress
Some operations can automatically print progress as they go. To enable this, set a {@link#ProgressCounter} on the #progress attribute.
Authors:
simon.sadedin@mcri.edu.au

Properties Summary

Properties
Type	Name and description
`java.io.File`	`indexFile`
`int`	`minMappingQuality`
`static boolean`	`progress`
`java.io.File`	`samFile`
`htsjdk.samtools.SamReader`	`samFileReader`
`java.io.InputStream`	`samStream` Only used when created from stream
`java.util.List<java.lang.String>`	`samples` List of samples in the BAM file.
`boolean`	`useMemoryMapping`
`boolean`	`verbose`

Constructor Summary

Constructors
Constructor and description
`SAM ()`
`SAM (java.io.InputStream ips)`
`SAM (java.lang.String fileName)`
`SAM (java.io.File file)`

Methods Summary

Methods
Type Params	Return Type	Name and description
	`Regions`	`asType(java.lang.Class clazz)`
	`java.util.Map<java.lang.String, java.lang.Integer>`	`basesAt(java.lang.String chr, int pos)` Return a Map with a key for each base observed at the given position, with the value being the number of times that base was observed.
	`void`	`close()` Close the underlying SamReader
	`int`	`countOf(java.lang.String chr, int pos, java.lang.String baseString)`
	`java.util.Map<java.lang.String, java.lang.Long>`	`countOnTarget(Regions targets)` Return a set of read counts indicating the counts of reads in that overlap the target region.
	`int`	`countPairs(gngs.Region r)` Count the number of read pairs in the given region
	`int`	`countPairs(java.lang.String chr, int start, int end)` Count the number of read pairs in the given region
	`int`	`coverage(java.lang.String chr, int pos, groovy.lang.Closure c)`
	`int`	`coverage(java.lang.String chr, int pos, int end, groovy.lang.Closure c)`
	`static int`	`coverage(htsjdk.samtools.SamReader r, java.lang.String chr, int pos, int end, groovy.lang.Closure c, int minMappingQuality)` Return the number of mapped reads overlapping the given position
	`RegulatingActor`	`coverageAsync(gngs.Region region, int minMAPQ, groovy.lang.Closure c)`
	`RegulatingActor`	`coverageAsync(Regions regions, int minMAPQ, groovy.lang.Closure c)`
	`void`	`coverageAsync(gngs.Region region, RegulatingActor sink, int minMAPQ)` Stream coverage values as SampleReadCount objects to the given actor from the given region(s).
	`int`	`coverageAsync(Regions regions, RegulatingActor sink, int minMAPQ)`
	`CoverageStats`	`coverageStatistics(IRegion r)` Create a CoverageStats object for the depth of coverage over the given region
	`CoverageStats`	`coverageStatistics(java.lang.String chr, int pos, int end)` Create a CoverageStats object for the depth of coverage over the given region
	`CoverageStats`	`coverageStatistics(Regions regions)`
	`void`	`eachPair(groovy.lang.Closure c)` Call the given closure for every pair of reads in a BAM file containing paired end reads.
	`void`	`eachPair(java.util.Map options, groovy.lang.Closure c)` Call the given closure for every pair of reads in a BAM file containing paired end reads.
	`void`	`eachPair(java.util.Map options, htsjdk.samtools.SAMRecordIterator iter, groovy.lang.Closure c)` Call the given closure for every pair of reads in a BAM file containing paired end reads.
	`void`	`eachPair(gngs.Region r, groovy.lang.Closure c)`
	`void`	`eachPair(java.lang.String chr, groovy.lang.Closure c)`
	`void`	`eachPair(java.util.Map options, java.lang.String chr, int start, int end, groovy.lang.Closure c)`
	`static void`	`eachRead(groovy.lang.Closure c)` Read a BAM or SAM file from standard input and call the given closure for each read contained therein.
	`void`	`eachRecord(java.util.Map options, groovy.lang.Closure c)` Iterate over each record in the same file in the order they are in the file
	`void`	`eachRecord(RegulatingActor<SAMRecord> actor)` Iterate over each record in the same file in the order they are in the file
	`void`	`eachRecord(gngs.Region region, RegulatingActor<java.util.List<SAMRecord>> actor)` Iterate over each record in the same file in the order they are in the file
	`void`	`eachRecord(int threads, groovy.lang.Closure c)` Call the given closure for each read in this alignment, using the given number of threads eg:
	`void`	`filter(groovy.lang.Closure c)` Filter the SAM/BAM file to include only the reads for which the given closure returns true.
	`void`	`filter(java.util.Map options, java.lang.String outputFile, groovy.lang.Closure c)` Filter the SAM/BAM file to include only the reads for which the given closure returns true
	`void`	`filterOrderedPairs(java.util.Map options, java.lang.String outputFileName, groovy.lang.Closure c)` Execute the given closure with an actor (parallel thread) set to write ordered pairs to the given output file, based on this BAM file.
	`java.lang.String`	`genotype(java.lang.String chr, int pos)` Use a simple thresholding approach to genotype SNPs at the given location
	`java.util.List<java.lang.String>`	`getContigList()` Returns: a list of contigs in the BAM file in sort order of the BAM file
	`Regions`	`getContigRegions()` Return the contigs of this BAM file as a set of regions
	`java.util.Map<java.lang.String, java.lang.Integer>`	`getContigs()` Returns: Map of contig name to size for all the contigs in this SAM
	`java.util.List<SAMReadGroupRecord>`	`getReadGroups()` Returns: Return the list of read groups present in the SAM file
	`java.util.List<java.lang.String>`	`getSamples()`
	`static void`	`index(java.io.File bamFile)` Create an index for the given BAM file
	`float`	`meanCoverage(java.lang.String chr, int pos, int end)`
	`void`	`movingWindow(int windowSize, java.lang.String chr, groovy.lang.Closure c, groovy.lang.Closure filterFn)` Call the given closure for each base position with a moving window of reads over that position
	`void`	`movingWindow(int windowSize, java.lang.String chr, int start, int end, groovy.lang.Closure c, groovy.lang.Closure filterFn)` Call the given closure for each base position with a moving window of reads over that position
	`htsjdk.samtools.SamReader`	`newReader(java.util.Map options)`
	`htsjdk.samtools.SAMFileWriter`	`newWriter(java.lang.String outputFileName)` Return a new SAMFileWriter configured with the same settings as this SAM.
	`Pileup`	`pileup(java.lang.String chr, int pos)`
	`void`	`pileup(java.lang.String chr, int start, int end, groovy.lang.Closure c)` Call the given closure once for each base between the start and end positions with a Pileup object representing the pileup state at that position.
	`PileupIterator`	`pileup(java.lang.String chr, int start, int end)` Create and return an iterator that iterates over Pileup objects over the given range.
	`PileupIterator`	`pileup(htsjdk.samtools.SamReader reader, java.lang.String chr, int start, int end)`
	`htsjdk.samtools.SAMRecord`	`queryMate(htsjdk.samtools.SamReader r, htsjdk.samtools.SAMRecord r1)`
	`int`	`size()` Count the total number of reads in the SAM file
	`java.lang.String`	`sniffGenomeBuild()` Probe the given BAM file to make a guess about what genome build it is generated from.
	`Regions`	`toPairRegions(java.lang.String chr, int start, int end, int maxSize)` Return read pairs from this SAM file that overlap the specified region as a Regions object - that is, as a set of genomic intervals.
	`java.util.List<QueryInterval>`	`toQueryIntervals(Regions regions)`
	`Regions`	`toRegions(gngs.Region overlapping)`
	`Regions`	`toRegions(java.lang.String chr, int start, int end)` Return reads from this SAM file that overlap the specified region as a Regions object - that is, as a set of genomic intervals.
	`java.lang.Object`	`withIterator(gngs.Region region, groovy.lang.Closure c)`
	`java.lang.Object`	`withIterator(groovy.lang.Closure c)`
	`java.lang.Object`	`withOrderedPairActor(java.util.Map options, java.lang.String outputFileName, groovy.lang.Closure c)` Execute the given closure with an actor set to write ordered pairs to the given output file, based on this BAM file.
	`java.lang.Object`	`withOrderedPairWriter(java.util.Map options, java.lang.String outputFileName, boolean sorted, groovy.lang.Closure c)`
	`java.lang.Object`	`withReader(groovy.lang.Closure c)`
	`java.lang.Object`	`withWriter(java.lang.String outputFileName, groovy.lang.Closure c)` Return a new SAMFileWriter configured with the same settings as this SAM.
	`java.lang.Object`	`withWriter(java.lang.String outputFileName, boolean sorted, groovy.lang.Closure c)`

Inherited Methods Summary

Inherited Methods
Methods inherited from class	Name
`class java.lang.Object`	`java.lang.Object#wait(long), java.lang.Object#wait(long, int), java.lang.Object#wait(), java.lang.Object#equals(java.lang.Object), java.lang.Object#toString(), java.lang.Object#hashCode(), java.lang.Object#getClass(), java.lang.Object#notify(), java.lang.Object#notifyAll()`

- Property Detail
  - java.io.File indexFile
  - int minMappingQuality
  - static boolean progress
  - java.io.File samFile
  - htsjdk.samtools.SamReader samFileReader
  - java.io.InputStream samStream
    
    Only used when created from stream
  - java.util.List<java.lang.String> samples
    
    List of samples in the BAM file. Note: this list can be overridden to associate different samples to the BAM files to those in the BAM header.
  - boolean useMemoryMapping
  - boolean verbose
- Constructor Detail
  - SAM()
  - SAM(java.io.InputStream ips)
  - SAM(java.lang.String fileName)
  - SAM(java.io.File file)
- Method Detail
  - Regions asType(java.lang.Class clazz)
  - @groovy.transform.CompileStatic java.util.Map<java.lang.String, java.lang.Integer> basesAt(java.lang.String chr, int pos)
    
    Return a Map with a key for each base observed at the given position, with the value being the number of times that base was observed. Additionally, a keys for deletions ('deletion') and total bases ('total') are set. @return
    Parameters:
    chr
    pos
  - void close()
    
    Close the underlying SamReader
  - @groovy.transform.CompileStatic int countOf(java.lang.String chr, int pos, java.lang.String baseString)
  - java.util.Map<java.lang.String, java.lang.Long> countOnTarget(Regions targets)
    
    Return a set of read counts indicating the counts of reads in that overlap the target region.
    todo:
    this is pretty inefficient compared to how it could be. It makes 2 passes through the data where it could do 1.
    
    Parameters:
    targets
    Returns:
    Map with keys on_target: reads overlapping target region, and bp_on_target: number of base pairs sequenced that overlap the target region, total: total count of reads.
  - int countPairs(gngs.Region r)
    
    Count the number of read pairs in the given region
    Parameters:
    r - region to count pairs over
    Returns:
    number of read pairs that overlap the region
  - @groovy.transform.CompileStatic int countPairs(java.lang.String chr, int start, int end)
    
    Count the number of read pairs in the given region
    Parameters:
    chr - chromsome of region
    start - start of region
    end - end of region
    Returns:
    number of read pairs that overlap the region
  - @groovy.transform.CompileStatic int coverage(java.lang.String chr, int pos, groovy.lang.Closure c)
  - @groovy.transform.CompileStatic int coverage(java.lang.String chr, int pos, int end, groovy.lang.Closure c)
  - @groovy.transform.CompileStatic static int coverage(htsjdk.samtools.SamReader r, java.lang.String chr, int pos, int end, groovy.lang.Closure c, int minMappingQuality)
    
    Return the number of mapped reads overlapping the given position
    Parameters:
    r - the SamReader (SAM / BAM file) containing reads
    chr - the sequence name / chromosome to query
    pos - the chromosomal position to query
    c - a filter to include or reject reads
    Returns:
    the number of reads overlapping the position in the file
  - @groovy.transform.CompileStatic RegulatingActor coverageAsync(gngs.Region region, int minMAPQ, @groovy.transform.stc.ClosureParams(value: SimpleType, options: gngs.SampleReadCount) groovy.lang.Closure c)
  - @groovy.transform.CompileStatic RegulatingActor coverageAsync(Regions regions, int minMAPQ, @groovy.transform.stc.ClosureParams(value: SimpleType, options: gngs.SampleReadCount) groovy.lang.Closure c)
  - @groovy.transform.CompileStatic void coverageAsync(gngs.Region region, RegulatingActor sink, int minMAPQ)
    
    Stream coverage values as SampleReadCount objects to the given actor from the given region(s).
  - @groovy.transform.CompileStatic int coverageAsync(Regions regions, RegulatingActor sink, int minMAPQ)
  - @groovy.transform.CompileStatic CoverageStats coverageStatistics(IRegion r)
    
    Create a CoverageStats object for the depth of coverage over the given region
  - @groovy.transform.CompileStatic CoverageStats coverageStatistics(java.lang.String chr, int pos, int end)
    
    Create a CoverageStats object for the depth of coverage over the given region
  - @groovy.transform.CompileStatic CoverageStats coverageStatistics(Regions regions)
  - @groovy.transform.CompileStatic void eachPair(@groovy.transform.stc.ClosureParams(value: SimpleType, options: [htsjdk.samtools.SAMRecord, htsjdk.samtools.SAMRecord]) groovy.lang.Closure c)
    
    Call the given closure for every pair of reads in a BAM file containing paired end reads.
    Note: the algorithm works by keeping a running buffer of reads, and iterating through the reads in order until each single read finds its mate. This means that reads having no mate accumulate in the buffer without ever being removed. Thus a large BAM file containing millions of unpaired reads could cause this method to use substantial ammounts of memory.
    Parameters:
    c - Closure to call
  - @groovy.transform.CompileStatic void eachPair(java.util.Map options, @groovy.transform.stc.ClosureParams(value: SimpleType, options: [htsjdk.samtools.SAMRecord, htsjdk.samtools.SAMRecord]) groovy.lang.Closure c)
    
    Call the given closure for every pair of reads in a BAM file containing paired end reads.
    Note: the algorithm works by keeping a running buffer of reads, and iterating through the reads in order until each single read finds its mate. This means that reads having no mate accumulate in the buffer without ever being removed. Thus a large BAM file containing millions of unpaired reads could cause this method to use substantial ammounts of memory.
    Parameters:
    c - Closure to call
  - @groovy.transform.CompileStatic void eachPair(java.util.Map options, htsjdk.samtools.SAMRecordIterator iter, @groovy.transform.stc.ClosureParams(value: SimpleType, options: [htsjdk.samtools.SAMRecord, htsjdk.samtools.SAMRecord]) groovy.lang.Closure c)
    
    Call the given closure for every pair of reads in a BAM file containing paired end reads.
    Note: the algorithm works by keeping a running buffer of reads, and iterating through the reads in order until each single read finds its mate. This means that reads having no mate accumulate in the buffer without ever being removed. Thus a large BAM file containing millions of unpaired reads could cause this method to use substantial ammounts of memory.
    Parameters:
    iter - iterator to consumer reads from
    c - Closure to call
  - void eachPair(gngs.Region r, groovy.lang.Closure c)
  - void eachPair(java.lang.String chr, groovy.lang.Closure c)
  - @groovy.transform.CompileStatic void eachPair(java.util.Map options, java.lang.String chr, int start, int end, groovy.lang.Closure c)
  - @groovy.transform.CompileStatic static void eachRead(groovy.lang.Closure c)
    
    Read a BAM or SAM file from standard input and call the given closure for each read contained therein.
    Parameters:
    c
  - @groovy.transform.CompileStatic void eachRecord(java.util.Map options, @groovy.transform.stc.ClosureParams(value: SimpleType, options: [htsjdk.samtools.SAMRecord]) groovy.lang.Closure c)
    
    Iterate over each record in the same file in the order they are in the file
    Parameters:
    c
  - @groovy.transform.CompileStatic void eachRecord(RegulatingActor<SAMRecord> actor)
    
    Iterate over each record in the same file in the order they are in the file
    Parameters:
    c
  - @groovy.transform.CompileStatic void eachRecord(gngs.Region region, RegulatingActor<java.util.List<SAMRecord>> actor)
    
    Iterate over each record in the same file in the order they are in the file
    Parameters:
    c
  - void eachRecord(int threads, groovy.lang.Closure c)
    
    Call the given closure for each read in this alignment, using the given number of threads eg: SAM sam = new SAM("test.bam") sam.eachRecord(5) { r -> println(r.readName) }
    Parameters:
    threads - number of threads to use
    c - closure to call
  - void filter(groovy.lang.Closure c)
    
    Filter the SAM/BAM file to include only the reads for which the given closure returns true. Output is written to stdout.
    Parameters:
    c - Closure that should return true for reads that will be included in the output BAM file
  - @groovy.transform.CompileStatic void filter(java.util.Map options, java.lang.String outputFile, @groovy.transform.stc.ClosureParams(value: SimpleType, options: [htsjdk.samtools.SAMRecord]) groovy.lang.Closure c)
    
    Filter the SAM/BAM file to include only the reads for which the given closure returns true
    Parameters:
    outputFile - the path to the output file
    c - Closure that should return true for reads that will be included in the output BAM file
  - @groovy.transform.CompileStatic void filterOrderedPairs(java.util.Map options, java.lang.String outputFileName, groovy.lang.Closure c)
    
    Execute the given closure with an actor (parallel thread) set to write ordered pairs to the given output file, based on this BAM file.
    If the closure returns a SAMRecordPair then the pair is written. If any other value is returned, the value is evaluated as a boolean and the original read pair is written if the boolean is true.
  - @groovy.transform.CompileStatic java.lang.String genotype(java.lang.String chr, int pos)
    
    Use a simple thresholding approach to genotype SNPs at the given location @return
    Parameters:
    chr
    pos
  - @groovy.transform.CompileStatic java.util.List<java.lang.String> getContigList()
    
    Returns:
    a list of contigs in the BAM file in sort order of the BAM file
  - @groovy.transform.CompileStatic Regions getContigRegions()
    
    Return the contigs of this BAM file as a set of regions @return
  - @groovy.transform.CompileStatic java.util.Map<java.lang.String, java.lang.Integer> getContigs()
    
    Returns:
    Map of contig name to size for all the contigs in this SAM
  - @groovy.transform.CompileStatic java.util.List<SAMReadGroupRecord> getReadGroups()
    
    Returns:
    Return the list of read groups present in the SAM file
  - java.util.List<java.lang.String> getSamples()
  - @groovy.transform.CompileStatic static void index(java.io.File bamFile)
    
    Create an index for the given BAM file
    Parameters:
    bamFile
  - @groovy.transform.CompileStatic float meanCoverage(java.lang.String chr, int pos, int end)
  - void movingWindow(int windowSize, java.lang.String chr, groovy.lang.Closure c, groovy.lang.Closure filterFn)
    
    Call the given closure for each base position with a moving window of reads over that position
    NOTE: Requires a BAM file sorted by position. Will not work with unsorted bam file.
    Parameters:
    windowSize
    chr
    c
  - @groovy.transform.CompileStatic void movingWindow(int windowSize, java.lang.String chr, int start, int end, groovy.lang.Closure c, groovy.lang.Closure filterFn)
    
    Call the given closure for each base position with a moving window of reads over that position
    NOTE: Requires a BAM file sorted by position. Will not work with unsorted bam file.
    Parameters:
    windowSize - the size of window to use in bp
    start - start position
    end - end position
    c - callback function to invoke
    filterFn - optional filter function to apply that filters out reads
  - @groovy.transform.CompileStatic htsjdk.samtools.SamReader newReader(java.util.Map options)
  - htsjdk.samtools.SAMFileWriter newWriter(java.lang.String outputFileName)
    
    Return a new SAMFileWriter configured with the same settings as this SAM. It is the caller's responsibility to close the writer.
    Parameters:
    outputFileName - Name of file to write to
    Returns:
    SAMFileWriter
  - @groovy.transform.CompileStatic Pileup pileup(java.lang.String chr, int pos)
  - @groovy.transform.CompileStatic void pileup(java.lang.String chr, int start, int end, groovy.lang.Closure c)
    
    Call the given closure once for each base between the start and end positions with a Pileup object representing the pileup state at that position.
    Parameters:
    chr
    start
    end
    c
  - @groovy.transform.CompileStatic PileupIterator pileup(java.lang.String chr, int start, int end)
    
    Create and return an iterator that iterates over Pileup objects over the given range.
    Parameters:
    chr - Chromsome of range to iterate over
    start - Start of range
    end - End of range
    Returns:
    Iterator for iterating over Pileup state in range
  - @groovy.transform.CompileStatic PileupIterator pileup(htsjdk.samtools.SamReader reader, java.lang.String chr, int start, int end)
  - @groovy.transform.CompileStatic htsjdk.samtools.SAMRecord queryMate(htsjdk.samtools.SamReader r, htsjdk.samtools.SAMRecord r1)
  - @groovy.transform.CompileStatic int size()
    
    Count the total number of reads in the SAM file
    Returns:
    total number of reads (not pairs, each pair is counted as 2 reads)
  - java.lang.String sniffGenomeBuild()
    
    Probe the given BAM file to make a guess about what genome build it is generated from. @return
  - @groovy.transform.CompileStatic Regions toPairRegions(java.lang.String chr, int start, int end, int maxSize)
    
    Return read pairs from this SAM file that overlap the specified region as a Regions object - that is, as a set of genomic intervals. Each region returned by this method spans from the start of the 5' read to the end of the 3' read.
    Reads that are missing a start or end alignment position are omitted. Unpaired reads are also omitted.
    If called without passing start or end, the start / end are interpreted as the beginning / end of the chromosome / reference sequence respectively.
    Returns:
    Regions object containing intervals representing all the reads in this SAM object
  - @groovy.transform.CompileStatic java.util.List<QueryInterval> toQueryIntervals(Regions regions)
  - Regions toRegions(gngs.Region overlapping)
  - @groovy.transform.CompileStatic Regions toRegions(java.lang.String chr, int start, int end)
    
    Return reads from this SAM file that overlap the specified region as a Regions object - that is, as a set of genomic intervals.
    Reads that are missing a start or end alignment position are omitted.
    If called without passing start or end, the start / end are interpreted as the beginning / end of the chromosome / reference sequence respectively.
    Returns:
    Regions object containing intervals representing all the reads in this SAM object
  - @groovy.transform.CompileStatic java.lang.Object withIterator(gngs.Region region, @groovy.transform.stc.ClosureParams(value: SimpleType, options: [htsjdk.samtools.SAMRecordIterator]) groovy.lang.Closure c)
  - @groovy.transform.CompileStatic java.lang.Object withIterator(@groovy.transform.stc.ClosureParams(value: SimpleType, options: [htsjdk.samtools.SAMRecordIterator]) groovy.lang.Closure c)
  - java.lang.Object withOrderedPairActor(java.util.Map options, java.lang.String outputFileName, groovy.lang.Closure c)
    
    Execute the given closure with an actor set to write ordered pairs to the given output file, based on this BAM file.
  - java.lang.Object withOrderedPairWriter(java.util.Map options, java.lang.String outputFileName, boolean sorted, groovy.lang.Closure c)
  - @groovy.transform.CompileStatic java.lang.Object withReader(groovy.lang.Closure c)
  - java.lang.Object withWriter(java.lang.String outputFileName, groovy.lang.Closure c)
    
    Return a new SAMFileWriter configured with the same settings as this SAM. It is the caller's responsibility to close the writer. In this version of the method the files are assumed to be pre-sorted*.
    Parameters:
    outputFileName - Name of file to write to
    Returns:
    SAMFileWriter
  - java.lang.Object withWriter(java.lang.String outputFileName, boolean sorted, groovy.lang.Closure c)

Summary:
Property
Constructor
Method

| Detail:
Property
Constructor
Method

Groovy Documentation

[Groovy] Class SAM

Progress

Properties Summary

Constructor Summary

Methods Summary

Inherited Methods Summary

Property Detail

java.io.File indexFile

int minMappingQuality

static boolean progress

java.io.File samFile

htsjdk.samtools.SamReader samFileReader

java.io.InputStream samStream

java.util.List<java.lang.String> samples

boolean useMemoryMapping

boolean verbose

Constructor Detail

SAM()

SAM(java.io.InputStream ips)

SAM(java.lang.String fileName)

SAM(java.io.File file)

Method Detail

Regions asType(java.lang.Class clazz)

@groovy.transform.CompileStatic java.util.Map<java.lang.String, java.lang.Integer> basesAt(java.lang.String chr, int pos)

void close()

@groovy.transform.CompileStatic int countOf(java.lang.String chr, int pos, java.lang.String baseString)

java.util.Map<java.lang.String, java.lang.Long> countOnTarget(Regions targets)

int countPairs(gngs.Region r)

@groovy.transform.CompileStatic int countPairs(java.lang.String chr, int start, int end)

@groovy.transform.CompileStatic int coverage(java.lang.String chr, int pos, groovy.lang.Closure c)

@groovy.transform.CompileStatic int coverage(java.lang.String chr, int pos, int end, groovy.lang.Closure c)

@groovy.transform.CompileStatic static int coverage(htsjdk.samtools.SamReader r, java.lang.String chr, int pos, int end, groovy.lang.Closure c, int minMappingQuality)

@groovy.transform.CompileStatic RegulatingActor coverageAsync(gngs.Region region, int minMAPQ, @groovy.transform.stc.ClosureParams(value: SimpleType, options: gngs.SampleReadCount) groovy.lang.Closure c)

@groovy.transform.CompileStatic RegulatingActor coverageAsync(Regions regions, int minMAPQ, @groovy.transform.stc.ClosureParams(value: SimpleType, options: gngs.SampleReadCount) groovy.lang.Closure c)

@groovy.transform.CompileStatic void coverageAsync(gngs.Region region, RegulatingActor sink, int minMAPQ)

@groovy.transform.CompileStatic int coverageAsync(Regions regions, RegulatingActor sink, int minMAPQ)

@groovy.transform.CompileStatic CoverageStats coverageStatistics(IRegion r)

@groovy.transform.CompileStatic CoverageStats coverageStatistics(java.lang.String chr, int pos, int end)

@groovy.transform.CompileStatic CoverageStats coverageStatistics(Regions regions)

@groovy.transform.CompileStatic void eachPair(@groovy.transform.stc.ClosureParams(value: SimpleType, options: [htsjdk.samtools.SAMRecord, htsjdk.samtools.SAMRecord]) groovy.lang.Closure c)

@groovy.transform.CompileStatic void eachPair(java.util.Map options, @groovy.transform.stc.ClosureParams(value: SimpleType, options: [htsjdk.samtools.SAMRecord, htsjdk.samtools.SAMRecord]) groovy.lang.Closure c)

@groovy.transform.CompileStatic void eachPair(java.util.Map options, htsjdk.samtools.SAMRecordIterator iter, @groovy.transform.stc.ClosureParams(value: SimpleType, options: [htsjdk.samtools.SAMRecord, htsjdk.samtools.SAMRecord]) groovy.lang.Closure c)

void eachPair(gngs.Region r, groovy.lang.Closure c)

void eachPair(java.lang.String chr, groovy.lang.Closure c)

@groovy.transform.CompileStatic void eachPair(java.util.Map options, java.lang.String chr, int start, int end, groovy.lang.Closure c)

@groovy.transform.CompileStatic static void eachRead(groovy.lang.Closure c)

@groovy.transform.CompileStatic void eachRecord(java.util.Map options, @groovy.transform.stc.ClosureParams(value: SimpleType, options: [htsjdk.samtools.SAMRecord]) groovy.lang.Closure c)

@groovy.transform.CompileStatic void eachRecord(RegulatingActor<SAMRecord> actor)

@groovy.transform.CompileStatic void eachRecord(gngs.Region region, RegulatingActor<java.util.List<SAMRecord>> actor)

void eachRecord(int threads, groovy.lang.Closure c)

void filter(groovy.lang.Closure c)

@groovy.transform.CompileStatic void filter(java.util.Map options, java.lang.String outputFile, @groovy.transform.stc.ClosureParams(value: SimpleType, options: [htsjdk.samtools.SAMRecord]) groovy.lang.Closure c)

@groovy.transform.CompileStatic void filterOrderedPairs(java.util.Map options, java.lang.String outputFileName, groovy.lang.Closure c)

@groovy.transform.CompileStatic java.lang.String genotype(java.lang.String chr, int pos)

@groovy.transform.CompileStatic java.util.List<java.lang.String> getContigList()

@groovy.transform.CompileStatic Regions getContigRegions()

@groovy.transform.CompileStatic java.util.Map<java.lang.String, java.lang.Integer> getContigs()

@groovy.transform.CompileStatic java.util.List<SAMReadGroupRecord> getReadGroups()

java.util.List<java.lang.String> getSamples()

@groovy.transform.CompileStatic static void index(java.io.File bamFile)

@groovy.transform.CompileStatic float meanCoverage(java.lang.String chr, int pos, int end)

void movingWindow(int windowSize, java.lang.String chr, groovy.lang.Closure c, groovy.lang.Closure filterFn)

@groovy.transform.CompileStatic void movingWindow(int windowSize, java.lang.String chr, int start, int end, groovy.lang.Closure c, groovy.lang.Closure filterFn)

@groovy.transform.CompileStatic htsjdk.samtools.SamReader newReader(java.util.Map options)

htsjdk.samtools.SAMFileWriter newWriter(java.lang.String outputFileName)

@groovy.transform.CompileStatic Pileup pileup(java.lang.String chr, int pos)

@groovy.transform.CompileStatic void pileup(java.lang.String chr, int start, int end, groovy.lang.Closure c)

@groovy.transform.CompileStatic PileupIterator pileup(java.lang.String chr, int start, int end)

@groovy.transform.CompileStatic PileupIterator pileup(htsjdk.samtools.SamReader reader, java.lang.String chr, int start, int end)

@groovy.transform.CompileStatic htsjdk.samtools.SAMRecord queryMate(htsjdk.samtools.SamReader r, htsjdk.samtools.SAMRecord r1)

@groovy.transform.CompileStatic int size()

java.lang.String sniffGenomeBuild()

@groovy.transform.CompileStatic Regions toPairRegions(java.lang.String chr, int start, int end, int maxSize)

@groovy.transform.CompileStatic java.util.List<QueryInterval> toQueryIntervals(Regions regions)

Regions toRegions(gngs.Region overlapping)

@groovy.transform.CompileStatic Regions toRegions(java.lang.String chr, int start, int end)

@groovy.transform.CompileStatic java.lang.Object withIterator(gngs.Region region, @groovy.transform.stc.ClosureParams(value: SimpleType, options: [htsjdk.samtools.SAMRecordIterator]) groovy.lang.Closure c)

@groovy.transform.CompileStatic java.lang.Object withIterator(@groovy.transform.stc.ClosureParams(value: SimpleType, options: [htsjdk.samtools.SAMRecordIterator]) groovy.lang.Closure c)

java.lang.Object withOrderedPairActor(java.util.Map options, java.lang.String outputFileName, groovy.lang.Closure c)

java.lang.Object withOrderedPairWriter(java.util.Map options, java.lang.String outputFileName, boolean sorted, groovy.lang.Closure c)