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
702b9276
Commit
702b9276
authored
Jul 18, 2017
by
Peter van 't Hof
Browse files
Fixing PR comments
parent
96d882f0
Changes
1
Hide whitespace changes
Inline
Side-by-side
biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/FastqSync.scala
View file @
702b9276
...
...
@@ -172,7 +172,7 @@ object FastqSync extends ToolCommand {
val
commandArgs
:
Args
=
parseArgs
(
args
)
val
subF
ixes
=
findR1R2Subfixes
(
commandArgs
.
refFastq1
,
commandArgs
.
refFastq2
)
idSuf
ixes
=
findR1R2Subfixes
(
commandArgs
.
refFastq1
,
commandArgs
.
refFastq2
)
val
refReader
=
new
FastqReader
(
commandArgs
.
refFastq1
)
val
AReader
=
new
FastqReader
(
commandArgs
.
inputFastq1
)
...
...
@@ -194,6 +194,13 @@ object FastqSync extends ToolCommand {
}
}
/**
* This method will look up the unique suffix for R1 and R2
*
* @param fastqR1 input R1 file
* @param fastqR2 Input R2 file
* @return subfix for (R1, R2)
*/
def
findR1R2Subfixes
(
fastqR1
:
File
,
fastqR2
:
File
)
:
(
String
,
String
)
=
{
val
refReader1
=
new
FastqReader
(
fastqR1
)
val
refReader2
=
new
FastqReader
(
fastqR2
)
...
...
@@ -208,6 +215,6 @@ object FastqSync extends ToolCommand {
}
/** Regex for capturing read ID ~ taking into account its read pair mark (if present) */
var
idSufixes
:
(
String
,
String
)
=
_
private
var
idSufixes
:
(
String
,
String
)
=
_
}
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