Fix a bug in cljam.algo.pileup/pileup

[alumi]

Summary

This PR fixes a bug in cljam.algo.pileup/pileup.

Problem

IllegalArgumentException in cljam.algo.pileup/pileup

java.lang.IllegalArgumentException: Value out of range for byte: 186

Cause

The qual field in cljam.io.pileup.PileupBase is declared as a byte because a phred-33 encoded base quality score never exceeds 93:

cljam/src/cljam/io/pileup.clj

Line 15 in 02addc4

^byte qual

The record is also constructed in cljam.algo.pileup:

cljam/src/cljam/algo/pileup.clj

Lines 85 to 94 in 02addc4

	(-> (PileupBase.
	(zero? relative-pos)
	(when (zero? relative-pos) (.mapq aln))
	base
	qual
	(flag/reversed? (.flag aln))
	(= ref-pos (.end aln))
	(when-not (number? indel) indel)
	(when (number? indel) indel)
	(.qname aln))

But quality scores can be 128 ~ 200 while piling alignments up with the option :ignore-overlaps false:

cljam/src/cljam/algo/pileup.clj

Lines 117 to 120 in 02addc4

	[(assoc r1 :qual (min 200 (+ q1 q2))) (assoc r2 :qual 0)]
	(if (<= q2 q1)
	[(assoc r1 :qual (int (* 0.8 q1))) (assoc r2 :qual 0)]
	[(assoc r1 :qual 0) (assoc r2 :qual (int (* 0.8 q2)))]))))

Changes

• Use short primitive type hinting instead of byte in cljam.io.pileup.PileupBase
• Fix broken tests related to pileup

Tests

• lein check 🆗
• lein test :all 🆗

[athos]

Good catch! Seems reasonable.

[totakke]

LGTM

[r6eve]

Looks good. Thank you for the modifications.

[alumi]

@athos @totakke @r6eve Thanks for your review! 😸