From a913c55e3dc3cc99b57b57828ee07ff9c0a43417 Mon Sep 17 00:00:00 2001
From: bow <bow@bow.web.id>
Date: Mon, 16 Feb 2015 10:49:31 +0100
Subject: [PATCH] Refactor syncIter logic
---
.../nl/lumc/sasc/biopet/tools/FastqSync.scala | 36 +++++++++----------
1 file changed, 17 insertions(+), 19 deletions(-)
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/FastqSync.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/FastqSync.scala
index 5096bdea8..d1b86906e 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/FastqSync.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/FastqSync.scala
@@ -128,25 +128,23 @@ object FastqSync extends ToolCommand {
(pre.headOption, seqA.headOption, seqB.headOption) match {
// where the magic happens!
case (Some(r), Some(a), Some(b)) =>
- // value of A iterator in the next recursion
- val nextA =
- // hold A if its head is not equal to reference
- if (a.fragId != r.fragId) {
- if (b.fragId == r.fragId) numDiscB += 1
- seqA
- // otherwise, go to next item
- } else seqA.tail
- // like A above
- val nextB =
- if (b.fragId != r.fragId) {
- if (a.fragId == r.fragId) numDiscA += 1
- seqB
- } else seqB.tail
- // write only if all IDs are equal
- if (a.fragId == r.fragId && b.fragId == r.fragId) {
- numKept += 1
- seqOutA.write(a)
- seqOutB.write(b)
+ val (nextA, nextB) = (a.fragId == r.fragId, b.fragId == r.fragId) match {
+ // all IDs are equal to ref
+ case (true, true) =>
+ numKept += 1
+ seqOutA.write(a)
+ seqOutB.write(b)
+ (seqA.tail, seqB.tail)
+ // B not equal to ref and A is equal, then we discard A and progress
+ case (true, false) =>
+ numDiscA += 1
+ (seqA.tail, seqB)
+ // A not equal to ref and B is equal, then we discard B and progress
+ case (false, true) =>
+ numDiscB += 1
+ (seqA, seqB.tail)
+ case (false, false) =>
+ (seqA, seqB)
}
syncIter(pre.tail, nextA, nextB)
// recursion base case: both iterators have been exhausted
--
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