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biopet.biopet
Commits
5f8092e9
Commit
5f8092e9
authored
Sep 15, 2014
by
Peter van 't Hof
Browse files
Fix counting on big files
parent
b36a4b5e
Changes
1
Hide whitespace changes
Inline
Side-by-side
biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/apps/BiopetFlagstat.scala
View file @
5f8092e9
...
...
@@ -105,7 +105,7 @@ object BiopetFlagstat extends Logging {
private
val
names
:
Map
[
Int
,
String
]
=
Map
()
private
var
functions
:
Array
[
SAMRecord
=>
Boolean
]
=
Array
()
private
var
totalCounts
:
Array
[
Long
]
=
Array
()
private
var
crossCounts
=
Array
.
ofDim
[
Int
](
1
,
1
)
private
var
crossCounts
=
Array
.
ofDim
[
Long
](
1
,
1
)
def
loadDefaultFunctions
{
addFunction
(
"All"
,
record
=>
true
)
...
...
@@ -149,7 +149,7 @@ object BiopetFlagstat extends Logging {
def
addFunction
(
name
:
String
,
function
:
SAMRecord
=>
Boolean
)
{
functionCount
+=
1
crossCounts
=
Array
.
ofDim
[
Int
](
functionCount
,
functionCount
)
crossCounts
=
Array
.
ofDim
[
Long
](
functionCount
,
functionCount
)
totalCounts
=
new
Array
[
Long
](
functionCount
)
val
temp
=
new
Array
[
SAMRecord
=>
Boolean
](
functionCount
)
for
(
t
<-
0
until
(
temp
.
size
-
1
))
temp
(
t
)
=
functions
(
t
)
...
...
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