cljam.algo.pileup — cljam 0.8.3

Functions to calculate pileup from the BAM.

->locus-pile clj

(->locus-pile chr [pos pile])

Convert a pile into cljam.io.pileup.LocusPile.

align-pileup-seqs clj

(align-pileup-seqs & xs)

Align multiple piled-up seqs.

basic-mpileup-pred clj

(basic-mpileup-pred min-mapq)

Basic predicate function for filtering alignments for mpileup.

create-mpileup clj

(create-mpileup in-sam out-mplp)

(create-mpileup in-sam in-ref out-mplp)

(create-mpileup in-sam in-ref out-mplp region)

(create-mpileup in-sam in-ref out-mplp region options)

Creates a mpileup file from the BAM file.

The following options are available:

• min-base-quality Minimum quality of called bases [13]
• min-map-quality Minimum quality of alignments [0]
• ignore-overlaps? Disable detecting overlapped bases of PE reads [false]

filter-by-base-quality clj

(filter-by-base-quality min-base-quality)

Returns a predicate for filtering piled-up reads by base quality at its position.

index-cigar clj

(index-cigar aln)

Align bases and base quality scores with the reference coordinate.

mpileup clj

(mpileup region options & sam-readers)

Pile up alignments from multiple sources.

The following options are available:

• min-base-quality Minimum quality of called bases [13]
• min-map-quality Minimum quality of alignments [0]
• ignore-overlaps? Disable detecting overlapped bases of PE reads [false]

pileup clj

(pileup sam-reader region)

(pileup sam-reader
        {:keys [chr start end] :or {start 1 end Integer/MAX_VALUE}}
        {:keys [min-base-quality min-map-quality ignore-overlaps? chunk-size]
         :or {min-base-quality 13
              min-map-quality 0
              ignore-overlaps? false
              chunk-size 5000}})

Piles up alignments in given region and returns a lazy sequence of cljam.io.pileup.LocusPiles.

The following options are available:

• min-base-quality Minimum quality of called bases [13]
• min-map-quality Minimum quality of alignments [0]
• ignore-overlaps? Disable detecting overlapped bases of PE reads [false]
• chunk-size Size of a chunk to pile up at once [5000]

pileup-seq clj

(pileup-seq start end alns)

Returns a lazy sequence that each element contains [position (alignments piled-up at the locus)].

resolve-base clj

(resolve-base ref-pos aln)

Find a piled-up base and an indel from an alignment.