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biopet.biopet
Commits
af39664b
Commit
af39664b
authored
Oct 10, 2014
by
Peter van 't Hof
Browse files
Switched to ToolCommand args parsing
parent
b443f31f
Changes
1
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Inline
Side-by-side
biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/apps/BiopetFlagstat.scala
View file @
af39664b
...
...
@@ -110,7 +110,8 @@ object BiopetFlagstat extends ToolCommand {
flagstatCollector
.
addFunction
(
"Mate in same strand"
,
record
=>
record
.
getReadPairedFlag
&&
record
.
getReadNegativeStrandFlag
&&
record
.
getMateNegativeStrandFlag
&&
record
.
getReferenceIndex
==
record
.
getMateReferenceIndex
)
flagstatCollector
.
addFunction
(
"Mate on other chr"
,
record
=>
record
.
getReadPairedFlag
&&
record
.
getReferenceIndex
!=
record
.
getMateReferenceIndex
)
logger
.
info
(
"Start reading file: "
+
commandArgs
.
inputFile
)
for
(
record
<-
iterSam
)
{
if
(
flagstatCollector
.
readsCount
%
1
e6
==
0
&&
flagstatCollector
.
readsCount
>
0
)
logger
.
info
(
"Reads prosessed: "
+
flagstatCollector
.
readsCount
)
...
...
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