Namespace refactoring

[totakke]

Changes namespaces of the whole source to make the project more simple.

• ns related to I/O => cljam.io
• ns related to algorithm like sorting => cljam.algo
• ns related to command-line tools => cljam.tools

These are breaking changes. Besides, unused items are removed. Please let me know if there's anything that you are concerned about.

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In the next stage, I intend to change public I/O APIs as follows:

• cljam.io => cljam.io.protocols
• cljam.io.sam and cljam.io.bam => cljam.io.sam
• cljam.io.vcf and cljam.io.bcf => cljam.io.vcf
• cljam.io.fasta and cljam.io.twobit => cljam.io.sequence

Current cljam.io is not user-friendly because it has unnecessary functions in some cases. Each format ns wraps protocol functions in the next version. To read SAM/BAM,

(require '[cljam.io.sam :as sam])

(with-open [rdr (sam/reader "foo.bam")]
  (sam/read-alignments rdr))

[codecov]

Codecov Report

Merging #83 into master will decrease coverage by 0.02%.
The diff coverage is 91.89%.

@@           Coverage Diff            @@
##           master    #83      +/-   ##
========================================
- Coverage   83.02%    83%   -0.03%     
========================================
  Files          62     63       +1     
  Lines        4160   4142      -18     
  Branches      430    432       +2     
========================================
- Hits         3454   3438      -16     
+ Misses        276    272       -4     
- Partials      430    432       +2

Impacted Files	Coverage Δ
src/cljam/common.clj	100% <ø> (ø)	⬆️
src/cljam/util.clj	79.22% <ø> (-1.27%)	⬇️
src/cljam/io/bam_index/core.clj	70.17% <0%> (ø)
src/cljam/io/dict/core.clj	58.33% <0%> (ø)
src/cljam/io/bed.clj	91.4% <0%> (ø)
src/cljam/io/sam/common.clj	100% <100%> (ø)
src/cljam/io/fasta/writer.clj	93.87% <100%> (ø)
src/cljam/io/sam/reader.clj	96.55% <100%> (ø)
src/cljam/algo/level.clj	88.31% <100%> (ø)
src/cljam/io/util/bgzf.clj	83.33% <100%> (ø)
... and 55 more

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[alumi]

Great changes! Looks much more organized.

[alumi]

unused items are removed. Please let me know if there's anything that you are concerned about.

Currently, I don't use them too. Thank you for removing.

In the next stage, I intend to change public I/O APIs as follows:

• cljam.io => cljam.io.protocols
• cljam.io.sam and cljam.io.bam => cljam.io.sam
• cljam.io.vcf and cljam.io.bcf => cljam.io.vcf
• cljam.io.fasta and cljam.io.twobit => cljam.io.sequence

I understand. some read/write-*** functions are triplicated now.

[alumi]

Merged. Thank you! 👍