# Functions
AlignmentToString returns a pargo pipeline.Receiver that formats slices of Alignment pointers into slices of strings representing these alignments according to the SAM file format.
ComposeFilters takes a Header and a slice of Filter functions, and successively calls these functions to generate the corresponding AlignmentFilter predicates.
CoordinateLess compares two alignments according to their coordinate.
Create a SAM file for output.
FormatComment writes a header comment line in a SAM file header section.
FormatHeaderLine writes a header line in a SAM file header section.
FormatString writes a SAM file TAG of type string.
FormatTag writes a SAM file TAG by appending its ASCII-string representation to out and returning the result, dispatching on the actual type of the given value.
IsHeaderUserTag determins whether this tag string represent a user-defined tag.
MergeSingleEndFilesSplitPerChromosome merges files containing single-end reads that were split with SplitSingleEndFilePerChromosome.
MergeSortedFilesSplitPerChromosome merges files that were split with SplitFilePerChromosome and sorted in coordinate order.
MergeUnsortedFilesSplitPerChromosome merges files that were split with SplitFilePerChromosome and are unsorted.
NewAlignment allocates and initializes an empty alignment.
NewHeader allocates and initializes an empty header.
NewSam allocates and initializes an empty SAM data set.
Open a SAM file for input.
ParseHeader parses a complete header in a SAM file.
ParseHeaderLineFromString parses a SAM header line from a string, except that entries are separated by white space instead of tabulators.
QNAMELess compares two alignments according to their query template name.
ScanCigarString converts a CIGAR string to a slice of CigarOperation.
SetSQLN sets the LN field value, assumming that the given record represents an @SQ line in the header section of a SAM file.
SkipHeader skips the complete header in a SAM file.
SplitFilePerChromosome splits a SAM file into: a file containing all unmapped reads, a file containing all pairs where reads map to different chromosomes, and a file per chromosome containing all pairs where the reads map to that chromosome.
SplitSingleEndFilePerChromosome splits a SAM file containing single-end reads into a file for the unmapped reads, and a file per chromosome, containing all reads that map to that chromosome.
SQLN returns he LN field value, assuming that the given record represents an @SQ line in the the header section of a SAM file.
StringToAlignment returns a pargo pipeline.Receiver that parses slices of strings representing alignments according to the SAM file format into slices of pointers to freshly allocated Alignment values.
# Constants
SAM file extensions.
CigarOperations contains all valid CIGAR operations.
Sorting orders.
SAM file extensions.
PCR or optical duplicate.
The SAM file format version and date strings supported by this library.
The SAM file format version and date strings supported by this library.
The first segment in the template.
Sorting orders.
The last segment in the template.
Template having multiple segments in sequencing.
SEQ of the next segment in the template being reverse complemented.
Next segment in the template unmapped.
Grouping orders.
Each segment properly aligned according to the aligner.
Not passing filters, such as platform/vendor quality controls.
Grouping orders.
Sorting orders.
Grouping orders.
SEQ being reversed complemented.
SAM file extensions.
Secondary alignment.
Supplementary alignment.
Sorting orders.
Segment unmapped.
Sorting orders.
# Variables
Symbols for some commonly used optional fields.
Symbols for some commonly used optional fields.
Symbols for some temporary fields.
Symbols for some commonly used optional fields.
Symbols for some commonly used optional fields.
Symbols for some temporary fields.
Symbols for some commonly used optional fields.
# Structs
An Alignment represents a single read alignment with mandatory and optional fields that can be contained in a SAM file alignment line.
AlignmentSorter is a helper for sorting Alignment slices that implements https://godoc.org/github.com/ExaScience/pargo/sort#StableSorter.
CigarOperation represents a CIGAR operation.
Header represents the information stored in the header section of a SAM file.
InputFile represents a SAM, BAM, or CRAM file for input.
OutputFile represents a SAM, BAM, or CRAM file for output.
Sam represents a complete SAM data set that can be contained in a SAM file.
A StringScanner can be used scan/parse ASCII strings representing lines in SAM files.
# Interfaces
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# Type aliases
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By is a type for comparison predicates on Alignment pointers.
ByteArray is a representation for byte arrays as stored in optional fields of read alignments lines using type H.
FieldParser is the signature for all parsers for optional fields in read alignment lines in SAM files.
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Reader is a bufio.Reader for a SAM, BAM or CRAM InputFile.
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Writer is a bufio.Writer for a SAM, BAM or CRAM OutputFile.