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biopet.biopet
Commits
1de25c35
Commit
1de25c35
authored
Oct 07, 2014
by
bow
Browse files
Make sure WipeReads also checks for single reads when filtering + writing
parent
84a7f167
Changes
1
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biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/apps/WipeReads.scala
View file @
1de25c35
...
...
@@ -328,6 +328,8 @@ object WipeReads extends MainCommand {
case
rec
:
SAMRecord
if
rec.getReadPairedFlag
=>
filteredOutSet
.
contains
(
rec
.
getReadName
+
"_"
+
rec
.
getAlignmentStart
).
isTrue
&&
filteredOutSet
.
contains
(
rec
.
getReadName
+
"_"
+
rec
.
getMateAlignmentStart
).
isTrue
case
rec
:
SAMRecord
if
!rec.getReadPairedFlag
=>
filteredOutSet
.
contains
(
rec
.
getReadName
+
"_"
+
rec
.
getAlignmentStart
).
isTrue
case
rec
:
String
=>
filteredOutSet
.
contains
(
rec
).
isTrue
case
_
=>
false
}
...
...
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