Use ByteBuffer wrapper instead of LSB protocol

[athos]

This PR is the first step of #289.

It replaces the use of ByteBuffer as an LSB protocol implementation with a new thin wrapper utility for ByteBuffer.

The modification policy here is to use the bare ByteBuffer methods whenever possible. The new wrapper namespace only collects functions that do what a single method of ByteBuffer cannot do. Most of the implementation code comes from the implementation of the LSB protocol.

[codecov]

Codecov Report

Attention: 3 lines in your changes are missing coverage. Please review.

Comparison is base (b72d8a9) 88.28% compared to head (2e027f0) 88.33%.

Files	Patch %	Lines
src/cljam/io/util/byte_buffer.clj	95.34%	2 Missing ⚠️
src/cljam/io/bcf/reader.clj	95.65%	1 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##           master     #290      +/-   ##
==========================================
+ Coverage   88.28%   88.33%   +0.04%     
==========================================
  Files          80       81       +1     
  Lines        6985     7028      +43     
  Branches      495      495              
==========================================
+ Hits         6167     6208      +41     
- Misses        323      325       +2     
  Partials      495      495              

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[athos]

Added accidentally omitted docstrings.

[athos]

Added some code to benchmark the performance of the BCF reader, and I've confirmed that the changes don't degrade the performance of the BAM/BCF readers:

• before

decode-bam-alignment-long-bench (sam_bench.clj:51)

  ["/Users/sohta/work/src/github.com/chrovis/cljam/.cavia/large.bam"]
  time: 21.659904 sec, sd: 62.121323 ms

decode-large-bcf-bench (vcf_bench.clj:14)

  ["/Users/sohta/work/src/github.com/chrovis/cljam/.cavia/large.bcf"]
  time: 24.589088 sec, sd: 515.149512 ms

• after

decode-bam-alignment-long-bench (sam_bench.clj:51)

  ["/Users/sohta/work/src/github.com/chrovis/cljam/.cavia/large.bam"]
  time: 19.811300 sec, sd: 63.591633 ms

decode-large-bcf-bench (vcf_bench.clj:14)

  ["/Users/sohta/work/src/github.com/chrovis/cljam/.cavia/large.bcf"]
  time: 24.433835 sec, sd: 878.578249 ms

[athos]

Rebased onto the latest master.

[alumi]

LGTM 👍 and thank you for adding the benchmarking codes!

[athos]

@ToshimitsuArai Just a reminder, if you have any feedback on the PR, feel free to let me know!

[ToshimitsuArai]

I apologize for being late reviewing, I just forget it and thank you for remind🙇‍♂️
LGTM and thanks for faster 👍

[athos]

Thank you both for taking the time to review this!