Documentation ¶
Overview ¶
Package samtools wraps the samtools cli to be used with Go.
Index ¶
Constants ¶
This section is empty.
Variables ¶
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Functions ¶
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.
Types ¶
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