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sam

package

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Versions in this module

v5

v5.1.3

Apr 27, 2022

v5.1.2

Feb 9, 2022

v5.1.1

Oct 4, 2021

Changes in this version

+ func MergeInputs(inputDir string, files []string) (*Header, []AlignmentFilter)

v5.1.0

Oct 1, 2021

Changes in this version

type Alignment

+ func (aln *Alignment) SetPG(pg interface{})

v5.0.2

May 19, 2021

v5.0.1

Feb 3, 2021

v5.0.0

Dec 8, 2020

Changes in this version

+ const BamExt

+ const Duplicate

+ const FileFormatDate

+ const FileFormatVersion

+ const First

+ const Last

+ const Multiple

+ const NextReversed

+ const NextUnmapped

+ const Proper

+ const QCFailed

+ const Reversed

+ const SamExt

+ const Secondary

+ const Supplementary

+ const Unmapped

+ var CC = utils.Intern("CC")

+ var CigarOperatorConsumesReadBases = map[byte]int32

+ var CigarOperatorConsumesReferenceBases = map[byte]int32

+ var LB = utils.Intern("LB")

+ var LIBID = utils.Intern("LIBID")

+ var NextREFID = utils.Intern("NextREFID")

+ var PG = utils.Intern("PG")

+ var PU = utils.Intern("PU")

+ var REFID = utils.Intern("REFID")

+ var RG = utils.Intern("RG")

+ func AlignmentToBytes(writer *OutputFile) pipeline.Filter

+ func BytesToAlignment(reader *InputFile) pipeline.Filter

+ func ComposeFilters(header *Header, hdrFilters []Filter) (receiver pipeline.Receiver)

+ func CoordinateLess(aln1, aln2 *Alignment) bool

+ func FormatAlignment(aln *Alignment, out []byte) []byte

+ func IsHeaderUserTag(code string) bool

+ func MergeSingleEndFilesSplitPerChromosome(inputPath, output, inputPrefix, inputExtension, outputFormat string, ...)

+ func MergeSortedFilesSplitPerChromosome(inputPath, output, inputPrefix, inputExtension, outputFormat string, ...)

+ func MergeSortedFilesSplitPerChromosomeWithoutSpreadFile(inputPath, output, inputPrefix, inputExtension, outputFormat string, ...)

+ func MergeUnsortedFilesSplitPerChromosome(inputPath, output, inputPrefix, inputExtension, outputFormat string, ...)

+ func ParseBamHeader(reader io.Reader) (*Header, []BAMReference)

+ func ParseHeaderLineFromString(line string) utils.StringMap

+ func QNAMELess(aln1, aln2 *Alignment) bool

+ func ReadLengthFromCigar(cigar []CigarOperation) int32

+ func ReferenceLengthFromCigar(cigar []CigarOperation) int32

+ func SQLN(record utils.StringMap) int32

+ func SetSQLN(record utils.StringMap, value int32)

+ func SkipSamHeader(reader *bufio.Reader)

+ func SplitFilePerChromosome(input, outputPath, outputPrefix, outputExtension string, contigGroupSize int)

+ func SplitSingleEndFilePerChromosome(input, outputPath, outputPrefix, outputExtension string, contigGroupSize int)

+ type Alignment struct

+ CIGAR []CigarOperation

+ FLAG uint16

+ MAPQ byte

+ PNEXT int32

+ POS int32

+ QNAME string

+ QUAL []byte

+ RNAME string

+ RNEXT string

+ SEQ Sequence

+ TAGS utils.SmallMap

+ TLEN int32

+ Temps utils.SmallMap

+ func ParseAlignment(s string) *Alignment

+ func ParseAlignmentFromBytes(s []byte) *Alignment

+ func (aln *Alignment) End() int32

+ func (aln *Alignment) FlagEvery(flag uint16) bool

+ func (aln *Alignment) FlagNotAny(flag uint16) bool

+ func (aln *Alignment) FlagNotEvery(flag uint16) bool

+ func (aln *Alignment) FlagSome(flag uint16) bool

+ func (aln *Alignment) IsDuplicate() bool

+ func (aln *Alignment) IsFirst() bool

+ func (aln *Alignment) IsLast() bool

+ func (aln *Alignment) IsMultiple() bool

+ func (aln *Alignment) IsNextReversed() bool

+ func (aln *Alignment) IsNextUnmapped() bool

+ func (aln *Alignment) IsProper() bool

+ func (aln *Alignment) IsQCFailed() bool

+ func (aln *Alignment) IsReversed() bool

+ func (aln *Alignment) IsSecondary() bool

+ func (aln *Alignment) IsSupplementary() bool

+ func (aln *Alignment) IsUnmapped() bool

+ func (aln *Alignment) LIBID() interface{}

+ func (aln *Alignment) NextREFID() int32

+ func (aln *Alignment) REFID() int32

+ func (aln *Alignment) RG() interface{}

+ func (aln *Alignment) SetLIBID(libid interface{})

+ func (aln *Alignment) SetNextREFID(refid int32)

+ func (aln *Alignment) SetREFID(refid int32)

+ func (aln *Alignment) SetRG(rg interface{})

+ type AlignmentFilter func(*Alignment) bool

+ type AlignmentSorter struct

+ func (s AlignmentSorter) Assign(p psort.StableSorter) func(i, j, len int)

+ func (s AlignmentSorter) Len() int

+ func (s AlignmentSorter) Less(i, j int) bool

+ func (s AlignmentSorter) NewTemp() psort.StableSorter

+ func (s AlignmentSorter) SequentialSort(i, j int)

+ type BAMReference struct

+ Length int32

+ Name string

+ func SkipBamHeader(reader io.Reader) []BAMReference

+ type By func(aln1, aln2 *Alignment) bool

+ func (by By) ParallelStableMerge(alns1, alns2 []*Alignment) (result []*Alignment)

+ func (by By) ParallelStableSort(alns []*Alignment)

+ type ByteArray []byte

+ type CigarOperation struct

+ Length int32

+ Operation byte

+ func ScanCigarString(cigar string) []CigarOperation

+ type Filter func(*Header) AlignmentFilter

+ type GroupingOrder string

+ const None

+ const Query

+ const Reference

+ type Header struct

+ CO []string

+ HD utils.StringMap

+ PG []utils.StringMap

+ RG []utils.StringMap

+ SQ []utils.StringMap

+ UserRecords map[string][]utils.StringMap

+ func NewHeader() *Header

+ func ParseSamHeader(reader *bufio.Reader) (hdr *Header)

+ func (hdr *Header) AddUserRecord(code string, record utils.StringMap)

+ func (hdr *Header) Contigs() (contigs []string, ok bool)

+ func (hdr *Header) EnsureHD() utils.StringMap

+ func (hdr *Header) EnsureUserRecords() map[string][]utils.StringMap

+ func (hdr *Header) FormatBam(out []byte) []byte

+ func (hdr *Header) FormatSam(out []byte) []byte

+ func (hdr *Header) HDGO() GroupingOrder

+ func (hdr *Header) HDSO() SortingOrder

+ func (hdr *Header) SetHDGO(value GroupingOrder)

+ func (hdr *Header) SetHDSO(value SortingOrder)

+ type InputFile struct

+ func Open(name string) *InputFile

+ func OpenIfExists(name string) (*InputFile, bool)

+ func (f *InputFile) Close()

+ func (f *InputFile) Data() interface{}

+ func (f *InputFile) Err() error

+ func (f *InputFile) Fetch(size int) int

+ func (f *InputFile) ParseAlignment(block []byte) *Alignment

+ func (f *InputFile) ParseHeader() *Header

+ func (f *InputFile) Prepare(ctx context.Context) int

+ func (f *InputFile) RunPipeline(output PipelineOutput, hdrFilters []Filter, sortingOrder SortingOrder)

+ func (f *InputFile) SkipHeader()

+ type OutputFile struct

+ func Create(name string, format string) *OutputFile

+ func (f *OutputFile) AddNodes(p *pipeline.Pipeline, header *Header, sortingOrder SortingOrder)

+ func (f *OutputFile) Close()

+ func (f *OutputFile) FormatAlignment(aln *Alignment, out []byte) []byte

+ func (f *OutputFile) FormatHeader(hdr *Header)

+ func (f *OutputFile) Write(p []byte) int

+ type PipelineInput interface

+ RunPipeline func(output PipelineOutput, filters []Filter, sortingOrder SortingOrder)

+ type PipelineOutput interface

+ AddNodes func(p *pipeline.Pipeline, header *Header, sortingOrder SortingOrder)

+ type Sam struct

+ Alignments []*Alignment

+ Header *Header

+ func NewSam() *Sam

+ func (sam *Sam) AddNodes(p *pipeline.Pipeline, header *Header, sortingOrder SortingOrder)

+ func (sam *Sam) NofBatches(n int)

+ func (sam *Sam) RunPipeline(output PipelineOutput, hdrFilters []Filter, sortingOrder SortingOrder)

+ type Sequence nibbles.Nibbles

+ func (seq Sequence) AsString() string

+ func (seq Sequence) Base(i int) (base byte)

+ func (seq Sequence) Len() int

+ func (seq Sequence) SetBase(i int, base byte)

+ func (seq Sequence) Slice(low, high int) Sequence

+ type SortingOrder string

+ const Coordinate

+ const Keep

+ const Queryname

+ const Unknown

+ const Unsorted

Other modules containing this package

github.com/exascience/elprep

github.com/exascience/elprep/v4