Versions in this module Expand all Collapse all v1 v1.0.6 Aug 24, 2018 Changes in this version + const BamExt + const CigarOperations + const CramExt + 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 LB = utils.Intern("LB") + var LIBID = utils.Intern("LIBID") + var PG = utils.Intern("PG") + var PU = utils.Intern("PU") + var REFID = utils.Intern("REFID") + var RG = utils.Intern("RG") + func AlignmentToString(p *pipeline.Pipeline, _ pipeline.NodeKind, _ *int) (receiver pipeline.Receiver, _ pipeline.Finalizer) + func ComposeFilters(header *Header, hdrFilters []Filter) (receiver pipeline.Receiver) + func CoordinateLess(aln1, aln2 *Alignment) bool + func FormatComment(out *bufio.Writer, code, comment string) error + func FormatHeaderLine(out *bufio.Writer, code string, record utils.StringMap) error + func FormatString(out *bufio.Writer, tag, value string) error + func FormatTag(out []byte, tag utils.Symbol, value interface{}) ([]byte, error) + func IsHeaderUserTag(code string) bool + func MergeSingleEndFilesSplitPerChromosome(inputPath, output, fai, fasta, inputPrefix, inputExtension string, ...) (err error) + func MergeSortedFilesSplitPerChromosome(inputPath, output, fai, fasta, inputPrefix, inputExtension string, ...) (err error) + func MergeUnsortedFilesSplitPerChromosome(inputPath, output, fai, fasta, inputPrefix, inputExtension string, ...) (err error) + func ParseHeaderLineFromString(line string) (utils.StringMap, error) + func QNAMELess(aln1, aln2 *Alignment) bool + func SQLN(record utils.StringMap) (int32, error) + func SetSQLN(record utils.StringMap, value int32) + func SkipHeader(reader *bufio.Reader) (lines int, err error) + func SplitFilePerChromosome(input, outputPath, outputPrefix, outputExtension, fai, fasta string) (err error) + func SplitSingleEndFilePerChromosome(input, outputPath, outputPrefix, outputExtension, fai, fasta string) (err error) + func StringToAlignment(p *pipeline.Pipeline, _ pipeline.NodeKind, _ *int) (receiver pipeline.Receiver, _ pipeline.Finalizer) + type Alignment struct + CIGAR string + FLAG uint16 + MAPQ byte + PNEXT int32 + POS int32 + QNAME string + QUAL string + RNAME string + RNEXT string + SEQ string + TAGS utils.SmallMap + TLEN int32 + Temps utils.SmallMap + func NewAlignment() *Alignment + 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) Format(out []byte) ([]byte, error) + 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) REFID() int32 + func (aln *Alignment) RG() interface{} + func (aln *Alignment) SetLIBID(libid interface{}) + 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 By func(aln1, aln2 *Alignment) bool + func (by By) ParallelStableSort(alns []*Alignment) + type ByteArray []byte + type CigarOperation struct + Length int32 + Operation byte + func ScanCigarString(cigar string) ([]CigarOperation, error) + type FieldParser func(*StringScanner, utils.Symbol) (utils.Symbol, interface{}) + 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 ParseHeader(reader *bufio.Reader) (hdr *Header, lines int, err error) + func (hdr *Header) AddUserRecord(code string, record utils.StringMap) + func (hdr *Header) EnsureHD() utils.StringMap + func (hdr *Header) EnsureUserRecords() map[string][]utils.StringMap + func (hdr *Header) Format(out *bufio.Writer) (err error) + 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, headerOnly bool) (*InputFile, error) + func (input *InputFile) Close() error + func (input *InputFile) SamReader() *Reader + type OutputFile struct + func Create(name, fai, fasta string) (*OutputFile, error) + func (output *OutputFile) Close() error + func (output *OutputFile) SamWriter() *Writer + type PipelineInput interface + RunPipeline func(output PipelineOutput, filters []Filter, sortingOrder SortingOrder) error + type PipelineOutput interface + AddNodes func(p *pipeline.Pipeline, header *Header, sortingOrder SortingOrder) + type Reader bufio.Reader + func (input *Reader) RunPipeline(output PipelineOutput, hdrFilters []Filter, sortingOrder SortingOrder) error + type Sam struct + Alignments []*Alignment + Header *Header + func NewSam() *Sam + func (sam *Sam) AddNodes(p *pipeline.Pipeline, header *Header, sortingOrder SortingOrder) + func (sam *Sam) Format(out *bufio.Writer) error + func (sam *Sam) RunPipeline(output PipelineOutput, hdrFilters []Filter, sortingOrder SortingOrder) error + type SortingOrder string + const Coordinate + const Keep + const Queryname + const Unknown + const Unsorted + type StringScanner struct + func (sc *StringScanner) Err() error + func (sc *StringScanner) Len() int + func (sc *StringScanner) ParseAlignment() *Alignment + func (sc *StringScanner) ParseByteArray(tag utils.Symbol) (utils.Symbol, interface{}) + func (sc *StringScanner) ParseChar(tag utils.Symbol) (utils.Symbol, interface{}) + func (sc *StringScanner) ParseFloat(tag utils.Symbol) (utils.Symbol, interface{}) + func (sc *StringScanner) ParseHeaderField() (tag, value string) + func (sc *StringScanner) ParseHeaderLine() utils.StringMap + func (sc *StringScanner) ParseInteger(tag utils.Symbol) (utils.Symbol, interface{}) + func (sc *StringScanner) ParseMandatoryField() string + func (sc *StringScanner) ParseNumericArray(tag utils.Symbol) (utils.Symbol, interface{}) + func (sc *StringScanner) ParseOptionalField() (tag utils.Symbol, value interface{}) + func (sc *StringScanner) ParseString(tag utils.Symbol) (utils.Symbol, interface{}) + func (sc *StringScanner) Reset(s string) + type Writer bufio.Writer + func (output *Writer) AddNodes(p *pipeline.Pipeline, header *Header, sortingOrder SortingOrder)