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biopet.biopet
Commits
f0cccdd0
Commit
f0cccdd0
authored
Aug 04, 2016
by
Sander van der Zeeuw
Browse files
Build in check for passing correct interval to the tool.
parent
8eb7deef
Changes
1
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Inline
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biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/ExtractAlignedFastq.scala
View file @
f0cccdd0
...
...
@@ -63,7 +63,7 @@ object ExtractAlignedFastq extends ToolCommand {
def
intFromCoord
(
s
:
String
)
:
Int
=
s
.
replaceAll
(
","
,
""
).
replaceAll
(
"\\."
,
""
).
toInt
inStrings
.
map
{
case
ptn1
(
chr
,
start
,
end
)
=>
new
Interval
(
chr
,
intFromCoord
(
start
),
intFromCoord
(
end
))
case
ptn1
(
chr
,
start
,
end
)
if
intFromCoord
(
end
)
>
intFromCoord
(
start
)
=>
new
Interval
(
chr
,
intFromCoord
(
start
),
intFromCoord
(
end
))
case
ptn2
(
chr
,
start
)
=>
val
startCoord
=
intFromCoord
(
start
)
new
Interval
(
chr
,
startCoord
,
startCoord
)
...
...
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