inference

package
v0.0.0-...-324d411 Latest Latest
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 Go to latest Published: May 16, 2019 License: MIT Imports: 22 Imported by: 0

Documentation

Index

Constants

View Source 
const (
	SAM_CIGAR_MATCH     = 0
	SAM_CIGAR_INSERT    = 1
	SAM_CIGAR_DEL       = 2
	SAM_CIGAR_SKIP      = 3
	SAM_CIGAR_SOFT_CLIP = 4
	SAM_CIGAR_HARD_CLIP = 5
)

Variables

View Source 
var DEBUG *bool
View Source 
var SIMULATED_DATA *bool

Functions

func BamThread 

func BamThread(b *BAMWriters)

func CheckSplitReads 

func CheckSplitReads(reads [][]*Alignment, centromeres map[string]Region)

* Iterate over all reads and compute secondary "split" reads for some of them

func DeAlignCrappyReads 

func DeAlignCrappyReads(reads [][]*Alignment)

func DoDumpToBam 

func DoDumpToBam(alignments [][]*Alignment, b *BAMWriters, debugTags bool, attach_bx bool)

func DoRFAForOneBarcode 

func DoRFAForOneBarcode(work *WorkUnit,
	bams *BAMWriters,
	ref *GoBwaReference,
	settings *GoBwaSettings,
	config *RFAConfig,
	stats *RFAStats,
	reads []fastqreader.FastQRecord)

func DumpToBams 

func DumpToBams(alignments *Data, b *BAMWriters)

func FindRead 

func FindRead(alignments [][]*Alignment, molecules []*CandidateMolecule, qname string)

func FixCigar 

func FixCigar(in []uint32) bam.Cigar

func GetAlignments 

func GetAlignments(ref *GoBwaReference, settings *GoBwaSettings, barcode_chains [][]ChainedHit, delta int, arena *Arena) ([][]*Alignment, [][]*Alignment)

returns a map from read id to a map of

func GetChains 

func GetChains(ref *GoBwaReference, settings *GoBwaSettings, reads_for_barcode []fastqreader.FastQRecord, arena *Arena, score_delta int) ([][]ChainedHit, string)

func HardClip 

func HardClip(seq []byte, qual []byte, cigar []uint32, reversed bool) ([]byte, []byte, []uint32)

Convert from "soft" clipping to "hard" clipping. Truncate the sequence and quality and convert "S" to "H" in teh cigar string.

func Lariat 

func Lariat(args LariatArgs)

func ReturnBuffer 

func ReturnBuffer(reads []fastqreader.FastQRecord)

func SetArgsForTests 

func SetArgsForTests(args LariatArgs)

func WorkerThread 

func WorkerThread(input chan *WorkUnit,
	bams *BAMWriters,
	ref *GoBwaReference,
	settings *GoBwaSettings,
	config *RFAConfig,
	stats *RFAStats,
	worker_lock *sync.RWMutex)

* This is a single "worker" thread. It tries to grab work units until it gets * nil, then it shuts down.

Types

type Alignment 

type Alignment struct {
	// contains filtered or unexported fields
}

func FixGetForTypeAlignment 

func FixGetForTypeAlignment(val interface{}) *Alignment

func GetSplitAlignment 

func GetSplitAlignment(primary *Alignment, alignments []*Alignment, centromeres map[string]Region) (*Alignment, float64)

func (*Alignment) IsUnmapped 

func (aln *Alignment) IsUnmapped() bool

func (*Alignment) Print 

func (aln *Alignment) Print()

type BAMWriter 

type BAMWriter struct {
	Writer  *bam.Writer
	Contigs map[string]*bam.Reference
	Record  bam.Record
}

func CreateBAM 

func CreateBAM(ref *gobwa.GoBwaReference, path, read_groups, sample_id string, firstChunk bool) (*BAMWriter, error)

func (*BAMWriter) AppendBam 

func (b *BAMWriter) AppendBam(aln *Alignment, primary *Alignment, debugTags bool, attach_bx bool)

type BAMWriters 

type BAMWriters struct {
	BarcodeSortedBam     *BAMWriter
	PositionBucketedBams map[string][]*BAMWriter
	// contains filtered or unexported fields
}

func CreateBAMs 

func CreateBAMs(ref *gobwa.GoBwaReference, basePath, read_groups, sample_id string, _positionChunkSize int, debugTags bool, firstChunk bool) (*BAMWriters, error)

func (*BAMWriters) AppendBams 

func (b *BAMWriters) AppendBams(aln *Alignment, primary *Alignment, debugTags bool, attach_bx bool)

func (*BAMWriters) Close 

func (b *BAMWriters) Close()

type ByPosition 

type ByPosition []*Alignment

types and functions to be able to sort a list of aligntments by position, must already be of the same contig otherwise it doesnt make sense

func (ByPosition) Len 

func (a ByPosition) Len() int

func (ByPosition) Less 

func (a ByPosition) Less(i, j int) bool

func (ByPosition) Swap 

func (a ByPosition) Swap(i, j int)

type CandidateMolecule 

type CandidateMolecule struct {
	// contains filtered or unexported fields
}

type ChainedHit 

type ChainedHit struct {
	// contains filtered or unexported fields
}

type Data 

type Data struct {
	// contains filtered or unexported fields
}

type LariatArgs 

type LariatArgs struct {
	Reads                 *string
	Improper_pair_penalty *float64
	SIMULATED_DATA        *bool
	Output                *string
	Read_groups           *string
	Sample_id             *string
	Threads               *int
	Max_bcs               *int
	DEBUG                 *bool
	PositionChunkSize     *int
	DebugTags             *bool
	DebugPrintMove        *bool
	Genome                *string
	Centromeres           *string
	Trim                  *int
	FirstChunk            *bool
}

type MapQData 

type MapQData struct {
	// contains filtered or unexported fields
}

type Move 

type Move struct {
	// contains filtered or unexported fields
}

type Optimizer 

type Optimizer struct {
	// contains filtered or unexported fields
}

func (Optimizer) GenerateMove 

func (o Optimizer) GenerateMove(accept_move func(p_curr float64, p_next float64) bool) optimizer.Optimizable

type OrderedAlignmentMap 

type OrderedAlignmentMap struct {
	// contains filtered or unexported fields
}

func FixGetForTypeOrderedAlignmentMap 

func FixGetForTypeOrderedAlignmentMap(val interface{}) *OrderedAlignmentMap

func NewOrderedAlignmentMap 

func NewOrderedAlignmentMap() *OrderedAlignmentMap

func (*OrderedAlignmentMap) Delete 

func (om *OrderedAlignmentMap) Delete(key int)

func (*OrderedAlignmentMap) Get 

func (om *OrderedAlignmentMap) Get(key int) *Alignment

func (*OrderedAlignmentMap) Iter 

func (om *OrderedAlignmentMap) Iter() []*Alignment

func (*OrderedAlignmentMap) IterKeys 

func (om *OrderedAlignmentMap) IterKeys() []int

func (*OrderedAlignmentMap) Len 

func (om *OrderedAlignmentMap) Len() int

func (*OrderedAlignmentMap) Set 

func (om *OrderedAlignmentMap) Set(key int, val *Alignment)

type OrderedMap 

type OrderedMap struct {
	// contains filtered or unexported fields
}

func FixGetForTypeOrderedMap 

func FixGetForTypeOrderedMap(val interface{}) *OrderedMap

func NewOrderedMap 

func NewOrderedMap() *OrderedMap

func StashAlignments 

func StashAlignments(a *OrderedMap) *OrderedMap

func (*OrderedMap) Delete 

func (om *OrderedMap) Delete(key int)

func (*OrderedMap) Get 

func (om *OrderedMap) Get(key int) interface{}

func (*OrderedMap) Iter 

func (om *OrderedMap) Iter() []interface{}

func (*OrderedMap) IterKeys 

func (om *OrderedMap) IterKeys() []int

func (*OrderedMap) Len 

func (om *OrderedMap) Len() int

func (*OrderedMap) Set 

func (om *OrderedMap) Set(key int, val interface{})

type RFAConfig 

type RFAConfig struct {
	// contains filtered or unexported fields
}

Holds configuration parameters for the optimizer. These to be constant after set in main.

type RFAStats 

type RFAStats struct {
	// contains filtered or unexported fields
}

* Holds statistics and coordination points for RFA

type Region 

type Region struct {
	// contains filtered or unexported fields
}

type SortSplitScoring 

type SortSplitScoring []SplitScoring

func (SortSplitScoring) Len 

func (a SortSplitScoring) Len() int

func (SortSplitScoring) Less 

func (a SortSplitScoring) Less(i, j int) bool

func (SortSplitScoring) Swap 

func (a SortSplitScoring) Swap(i, j int)

type SplitScoring 

type SplitScoring struct {
	// contains filtered or unexported fields
}

type WorkUnit 

type WorkUnit struct {
	// contains filtered or unexported fields
}

* Holds a single unit of "work" to be processed by an RFA thread

Source Files

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