Fix parser generation not to interpret unnecessary data when calculat…

[niyarin]

To fix #240.
I improved index generation speed by changing parsers in read-file-offsets for vcf and bcf.

• Changed that of bcf not to interpret sample
• Changed it to: shallow in bcf and changed the end of the mutation to use rlen.

vcf benchmark

> bcftools view ALL.chr22.shapeit2_integrated_snvindels_v2a_27022019.GRCh38.phased.vcf.gz  |head -n 1000 > /tmp/index-bench.vcf
> bgzip /tmp/index-bench.vcf

• PR version

user=> (quick-bench
  #_=> (vcf-indexer/create-index
  #_=>        "/tmp/index-bench.vcf.gz"
  #_=>        "/tmp/index-bench.vcf.gz.csi"
  #_=>        {:shift 14 :depth 5}))
Evaluation count : 6 in 6 samples of 1 calls.
             Execution time mean : 192.050578 ms
    Execution time std-deviation : 9.026152 ms
   Execution time lower quantile : 183.364991 ms ( 2.5%)
   Execution time upper quantile : 205.642765 ms (97.5%)
                   Overhead used : 13.876721 ns

• old version

user=> (quick-bench
  #_=> (vcf-indexer/create-index
  #_=>        "/tmp/index-bench.vcf.gz"
  #_=>        "/tmp/index-bench.vcf.gz.csi"
  #_=>        {:shift 14 :depth 5}))
Evaluation count : 6 in 6 samples of 1 calls.
             Execution time mean : 9.188136 sec
    Execution time std-deviation : 29.107864 ms
   Execution time lower quantile : 9.143654 sec ( 2.5%)
   Execution time upper quantile : 9.217992 sec (97.5%)
                   Overhead used : 13.904601 ns

bcf benchmark

> bcftools view /tmp/index-bench.vcf.gz  -o /tmp/index-bench.bcf

• PR version

user=> (quick-bench
  #_=> (vcf-indexer/create-index
  #_=>        "/tmp/index-bench.bcf"
  #_=>        "/tmp/index-bench.bcf.csi"
  #_=>        {:shift 14 :depth 5}))
Evaluation count : 48 in 6 samples of 8 calls.
             Execution time mean : 15.261828 ms
    Execution time std-deviation : 544.830560 µs
   Execution time lower quantile : 14.609601 ms ( 2.5%)
   Execution time upper quantile : 15.972899 ms (97.5%)
                   Overhead used : 14.402711 ns

• old version
• Give up because it takes too long.

[codecov]

Codecov Report

Merging #241 (3e33bcd) into master (2902078) will not change coverage.
The diff coverage is 100.00%.

@@           Coverage Diff           @@
##           master     #241   +/-   ##
=======================================
  Coverage   88.70%   88.70%           
=======================================
  Files          76       76           
  Lines        6305     6305           
  Branches      438      438           
=======================================
  Hits         5593     5593           
  Misses        274      274           
  Partials      438      438           

Impacted Files	Coverage Δ
src/cljam/io/bcf/reader.clj	90.57% <100.00%> (ø)
src/cljam/io/vcf/reader.clj	87.73% <100.00%> (ø)

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[alumi]

LGTM 👍 Thanks!!

[xckitahara]

LGTM:+1:

[niyarin]

Thank you for reviewing.