AlignmentToBytes returns a pargo pipeline.Filter that formats slices of Alignment pointers into slices of bytes representing these alignments according to the SAM/BAM file format.

BytesToAlignment returns a pargo pipeline.Filter that parses slices of bytes representing alignments according to the SAM/BAM file format into slices of pointers to freshly allocated Alignment values.

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 or BAM file for output.

FormatAlignment writes a SAM file read alignment line by appending its ASCII-string representation to out and returning the result.

IsHeaderUserTag determins whether this tag string represent a user-defined tag.

mergeInputs handles merging of sam/bam files that are passed as inputs to the elPrep sfm command.It reads the headers from the files and attempts merging them into a new header object.

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.

NewHeader allocates and initializes an empty header.

NewSam allocates and initializes an empty SAM data set.

Open a SAM or BAM file for input.

OpenIfExists a SAM or BAM file for input, returning false if it doesn't exist.

ParseAlignment parses a SAM alignment from its string representation.

ParseAlignmentFromBytes parses a SAM alignment from its string representation.

ParseBamHeader 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.

ParseSamHeader parses a complete header in a SAM file.

QNAMELess compares two alignments according to their query template name.

ReadLengthFromCigar sums the lengths of all CIGAR operations that consume read bases.

ReferenceLengthFromCigar sums the lengths of all CIGAR operations that consume reference bases.

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.

SkipBamHeader skips the complete header in a BAM file.

SkipSamHeader 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.

SAM file extensions.

Sorting orders.

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.

Symbols for some commonly used optional fields.

CigarOperatorConsumesReadBases maps operators that consume read bases to 1.

CigarOperatorConsumesReferenceBases maps operators that consume reference bases to 1.

Symbols for some commonly used optional fields.

Symbols for some temporary 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.

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.

BAMReference is a an entry in a slice of BAM-encoded sequence dictionary entries.

CigarOperation represents a CIGAR operation.

Header represents the information stored in the header section of a SAM file.

Sam represents a complete SAM data set that can be contained in a SAM or BAM file.

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.

Sequence encodes a SAM segment SEQuence as in the BAM format.