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biopet.biopet
Commits
34b35a99
Commit
34b35a99
authored
Aug 24, 2016
by
Peter van 't Hof
Browse files
added exextion on from region
parent
97803088
Changes
1
Hide whitespace changes
Inline
Side-by-side
biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/ExtractAlignedFastq.scala
View file @
34b35a99
...
...
@@ -63,7 +63,9 @@ object ExtractAlignedFastq extends ToolCommand {
def
intFromCoord
(
s
:
String
)
:
Int
=
s
.
replaceAll
(
","
,
""
).
replaceAll
(
"\\."
,
""
).
toInt
inStrings
.
map
{
case
ptn1
(
chr
,
start
,
end
)
if
intFromCoord
(
end
)
>
intFromCoord
(
start
)
=>
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
ptn1
(
chr
,
start
,
end
)
if
intFromCoord
(
end
)
<
intFromCoord
(
start
)
=>
throw
new
IllegalStateException
(
s
"end is higher then start: $chr:$start-$end"
)
case
ptn2
(
chr
,
start
)
=>
val
startCoord
=
intFromCoord
(
start
)
new
Interval
(
chr
,
startCoord
,
startCoord
)
...
...
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