BED file reader/writer

[alumi]

BED file reader/writer

Added BED file reader.
Format of BED file is based on https://genome.ucsc.edu/FAQ/FAQformat#format1

e.g.

(def bed
  (with-open [r (clojure.java.io/reader "PATH/TO/BED/FILE")]
    (doall (cljam.bed/read-fields r))))
;; cljam.bed/read-fields returns a lazy sequence of maps

bed => `({:chr "chr1" :start 1 :end 100 :name "Plus1" :score 0 :strand :plus :thick-start 1 :thick-end 0
         :item-rgb "255,0,0" :block-count 2 :block-sizes [10 90] :block-starts [0 10]}
        {:chr "chr2" :start 1 :end 2000 ...} ...)

(with-open [w (clojure.java.io/writer "PATH/TO/BED/FILE")]
  (cljam.bed/write-fields w bed))
;; supported writer

(with-open [r (cljam.bam/reader "PATH/TO/BAM/FILE")]
  (cljam.io/read-alignments r (first bed)) => `({:qname "Read1" :flags 4 :rname "chr1" ...} ...))
;; Map of BED fields can be used for range-based querying

Range-based query

BED file uses zero-based index and end index is exclusive,
which means that chr1 0 3 represents first three bases of chromosome 1.
Currently, cljam uses one-based index and inclusive end for BAM APIs,
zero-based index and exclusive end for FASTA and pileup APIs.

To provide consistent APIs, this PR unifies the APIs as zero-based one-based index and inclusive end.
Thus, {:chr "chr1" :start 1 :end 3} represents first three bases of chromosome 1.

Please be aware that this is a destructive change!

[totakke]

To provide consistent APIs, this PR unifies the APIs as zero-based index and inclusive end.

Is "zero-based index" a typo for "one-based index"?

This change is destructive as you say. I think this PR should be merged after release of v0.1.6 (and bump up to v0.2.0-SNAPSHOT).

[alumi]

To provide consistent APIs, this PR unifies the APIs as zero-based index and inclusive end.

Is "zero-based index" a typo for "one-based index"?

Sorry about the mistake 🙇 It's fixed now.

bump up to v0.2.0-SNAPSHOT

LGTM:+1: I have some projects depending on v0.1.6-SHAPSHOT..

[totakke]

I've added some comments for code format. Functions of BED I/O have no problems.

[totakke]

Please use cstr as an aliase of clojure.string in cljam project.

[totakke]

arg vec and docstring are reverse.

[totakke]

arg vec and docstring are reverse.

[alumi]

Thank you for your advice. I've fixed them and rebased.

[totakke]

Thank you for the fixes. I've just merged this PR.