samtools

func Pileup ¶

func Pileup(ctx context.Context, templateFasta fasta.Record, samAlignments io.Reader, w io.Writer) error

Pileup generates a pileup file from sam alignments. Specifically, it runs the following commands, with the sam alignments in stdin and the templateFasta written to a temporary file:

`samtools view -bF 4 | samtools sort - | samtools mpileup -f tmpFile.fasta -`

The first samtools view removes unmapped sequences, the sort sorts the sequences for piping into pileup, and the final command builds the pileup file.

func PileupChanneled ¶

func PileupChanneled(ctx context.Context, templateFasta fasta.Record, samChan <-chan sam.Alignment, w io.Writer) error

PileupChanneled processes SAM alignments from a channel and sends pileup lines to another channel.