Add FASTQ=>FASTA, SAM=>FASTQ conversions.

[alumi]

Summary

Add converting functions for different contents.

• FASTQ(:name, :sequence, :quality) => FASTA/2BIT (:name :sequence)
• SAM/BAM (:qname, :seq, :qual ...) => FASTQ (:name, :sequence, :quality)
  • implemented converting like samtools fastq
  • can output to 1~3 FASTQ files
    • 1 (all primary alignments)
    • 2 (R1 and R2)
    • 3 (R1,R2 and others)

Tests

• lein test :all 🆗

[codecov]

Codecov Report

Merging #129 into master will increase coverage by 0.19%.
The diff coverage is 94.18%.

@@            Coverage Diff             @@
##           master     #129      +/-   ##
==========================================
+ Coverage   85.06%   85.25%   +0.19%     
==========================================
  Files          69       69              
  Lines        4285     4361      +76     
  Branches      417      420       +3     
==========================================
+ Hits         3645     3718      +73     
  Misses        223      223              
- Partials      417      420       +3

Impacted Files	Coverage Δ
src/cljam/tools/cli.clj	53.28% <33.33%> (-0.39%)	⬇️
src/cljam/algo/convert.clj	90% <96.38%> (+12.72%)	⬆️

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[totakke]

Thank you. I confirmed the behavior. However, I feel confusion about output args of convert... That doesn't seem intuitive, but what is better way...

Anyway, please remove unused requires.

[totakke]

cljam.io.sam and cljam.io.sam.util.sequence don't seem to be used.

[totakke]

Thanks for the fix.

[alumi]

Thank you for the helpful discussion!