cljam.algo.pileup.mpileup — cljam 0.6.1-SNAPSHOT

basic-mpileup-pred clj

(basic-mpileup-pred {:keys [flag]})

Basic predicate function for filtering alignments for mpileup.

correct-overlapped-reads clj

(correct-overlapped-reads pile)

Correct quality of two overlapped mate reads in piled-up reads.

create-mpileup clj

(create-mpileup f fa-rdr bam-reader)

Creates a mpileup file from the BAM file.

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.

gen-mpileup clj

(gen-mpileup rname locus [ref-base :as refs] reads)

Compute mpileup info from piled-up reads and reference.

pileup clj

(pileup bam-reader region)

(pileup ref-reader bam-reader {:keys [chr start end] :or {start -1 end -1}})

Returns a lazy sequence of MPileupElement calculated from FASTA and BAM.

pileup* clj

(pileup* refseq {:keys [chr start end]} & aln-seqs)

Internal mpileup function independent from I/O. Can take multiple alignments seqs.

pileup-seq clj

(pileup-seq start end reads)

Returns a lazy sequence that each element contains reads piled-up at the locus.

substitute-qual clj

(substitute-qual q [op x])

Substitute base quality with mpileup index.

substitute-seq clj

(substitute-seq [r & refs] s [op x xs])

Substitute sequence with mpileup index.

to-mpileup clj

(to-mpileup x)

Stringify mpileup sequence.

transpose-pile clj

(transpose-pile p)

Converts a pile {:pile [{:seq SEQ, :qual QUAL, :read READ}]} into {:seq [], :qual [], :reads []}.