Skip to content
GitLab
Projects
Groups
Snippets
/
Help
Help
Support
Community forum
Keyboard shortcuts
?
Submit feedback
Contribute to GitLab
Sign in
Toggle navigation
Menu
Open sidebar
Mirrors
biopet.biopet
Commits
c8e494d2
Commit
c8e494d2
authored
Oct 06, 2014
by
bow
Browse files
Update SAMRecord equality test to test as file is iterated
parent
657702dc
Changes
1
Hide whitespace changes
Inline
Side-by-side
biopet-framework/src/test/scala/nl/lumc/sasc/biopet/core/apps/WipeReadsUnitTest.scala
View file @
c8e494d2
...
...
@@ -225,8 +225,8 @@ class WipeReadsUnitTest extends Assertions {
writeFilteredBAM
(
mockFilterOutFunc
,
sbam01
,
outBAM
)
val
exp
=
new
SAMFileReader
(
sbam03
).
asScala
val
obs
=
new
SAMFileReader
(
outBAM
).
asScala
val
res
=
for
((
e
,
o
)
<-
exp
.
zip
(
obs
))
yield
e
.
getSAMString
===
o
.
getSAMString
assert
(
res
.
reduceLeft
(
_
&&
_
)
)
for
((
e
,
o
)
<-
exp
.
zip
(
obs
))
assert
(
e
.
getSAMString
===
o
.
getSAMString
)
assert
(
outBAM
.
exists
)
assert
(
outBAMIndex
.
exists
)
}
...
...
@@ -244,8 +244,8 @@ class WipeReadsUnitTest extends Assertions {
writeFilteredBAM
(
mockFilterOutFunc
,
sbam01
,
outBAM
,
filteredOutBAM
=
filteredOutBAM
)
val
exp
=
new
SAMFileReader
(
sbam04
).
asScala
val
obs
=
new
SAMFileReader
(
filteredOutBAM
).
asScala
val
res
=
for
((
e
,
o
)
<-
exp
.
zip
(
obs
))
yield
e
.
getSAMString
===
o
.
getSAMString
assert
(
res
.
reduceLeft
(
_
&&
_
)
)
for
((
e
,
o
)
<-
exp
.
zip
(
obs
))
assert
(
e
.
getSAMString
===
o
.
getSAMString
)
assert
(
outBAM
.
exists
)
assert
(
outBAMIndex
.
exists
)
assert
(
filteredOutBAM
.
exists
)
...
...
@@ -261,8 +261,8 @@ class WipeReadsUnitTest extends Assertions {
writeFilteredBAM
(
mockFilterOutFunc
,
pbam01
,
outBAM
)
val
exp
=
new
SAMFileReader
(
pbam03
).
asScala
val
obs
=
new
SAMFileReader
(
outBAM
).
asScala
val
res
=
for
((
e
,
o
)
<-
exp
.
zip
(
obs
))
yield
e
.
getSAMString
===
o
.
getSAMString
assert
(
res
.
reduceLeft
(
_
&&
_
)
)
for
((
e
,
o
)
<-
exp
.
zip
(
obs
))
assert
(
e
.
getSAMString
===
o
.
getSAMString
)
assert
(
outBAM
.
exists
)
assert
(
outBAMIndex
.
exists
)
}
...
...
Write
Preview
Supports
Markdown
0%
Try again
or
attach a new file
.
Cancel
You are about to add
0
people
to the discussion. Proceed with caution.
Finish editing this message first!
Cancel
Please
register
or
sign in
to comment