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biopet.biopet
Commits
3f86deaf
Commit
3f86deaf
authored
9 years ago
by
Sander van der Zeeuw
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changed error messages spelling
parent
93d87c58
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public/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/ValidateFastq.scala
+4
-4
4 additions, 4 deletions
.../main/scala/nl/lumc/sasc/biopet/tools/ValidateFastq.scala
with
4 additions
and
4 deletions
public/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/ValidateFastq.scala
+
4
−
4
View file @
3f86deaf
...
...
@@ -53,7 +53,7 @@ object ValidateFastq extends ToolCommand {
for
(
recordR1
<-
readFq1
.
iterator
())
{
counter
+=
1
if
(
readFq2
.
map
(
_
.
hasNext
)
==
Some
(
false
))
throw
new
IllegalStateException
(
"R2
ha
s less reads then R1"
)
throw
new
IllegalStateException
(
"R2
contain
s less reads then R1"
)
//Getting R2 record, None if it's single end
val
recordR2
=
readFq2
.
map
(
_
.
next
())
...
...
@@ -76,7 +76,7 @@ object ValidateFastq extends ToolCommand {
//if R2 is longer then R1 print an error code and exit the tool
if
(
readFq2
.
map
(
_
.
hasNext
)
==
Some
(
true
))
throw
new
IllegalStateException
(
"R2
ha
s more reads then R1"
)
throw
new
IllegalStateException
(
"R2
contain
s more reads then R1"
)
logger
.
info
(
s
"Possible quality encodings found: ${getPossibleEncodings.mkString("
,
")}"
)
...
...
@@ -159,7 +159,7 @@ object ValidateFastq extends ToolCommand {
case
_
=>
throw
new
IllegalStateException
(
s
"Non IUPAC symbols identified"
)
}
if
(
record
.
getReadString
.
size
!=
record
.
getBaseQualityString
.
size
)
throw
new
IllegalStateException
(
s
"Sequence length do not match quality length"
)
throw
new
IllegalStateException
(
s
"Sequence length do
es
not match quality length"
)
}
/**
...
...
@@ -174,6 +174,6 @@ object ValidateFastq extends ToolCommand {
if
(!(
id1
==
id2
||
id1
.
stripSuffix
(
"/1"
)
==
id2
.
stripSuffix
(
"/2"
)
||
id1
.
stripSuffix
(
".1"
)
==
id2
.
stripSuffix
(
".2"
)))
throw
new
IllegalStateException
(
s
"
s
equence
H
eaders do
es
not match. R1: '${r1.getReadHeader}', R2: '${r2.getReadHeader}'"
)
throw
new
IllegalStateException
(
s
"
S
equence
h
eaders do not match. R1: '${r1.getReadHeader}', R2: '${r2.getReadHeader}'"
)
}
}
\ No newline at end of file
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