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biopet.biopet
Commits
1ac69d32
Commit
1ac69d32
authored
Jul 03, 2015
by
Peter van 't Hof
Browse files
Fix code style warnings
parent
33f56126
Changes
2
Hide whitespace changes
Inline
Side-by-side
public/biopet-framework/src/main/resources/nl/lumc/sasc/biopet/core/report/main.ssp
View file @
1ac69d32
...
...
@@ -11,7 +11,7 @@
def createMenu(page: ReportPage, path: List[String] = Nil, first: Boolean = true): String = {
val buffer: StringBuffer = new StringBuffer()
if (page.subPages.
size > 0
){
if (page.subPages.
nonEmpty
){
buffer.append("
<ul
class=
\"dropdown-menu\"
>
")
}
...
...
@@ -22,14 +22,14 @@
}
buffer.append
("<
li
")
if
(
subPage._2.subPages.
size
>
0
) buffer.append(" class=\"dropdown-submenu\"")
if
(
subPage._2.subPages.
nonEmpty
)
buffer.append
("
class=
\"dropdown-submenu\"")
buffer.append
("
><a
href=
\""
+
href
+
"\"")
if
(
first
)
buffer.append
("
tabindex=
\"-1\"")
buffer.append
("
>
" + subPage._1 + "
</a>
")
buffer.append(createMenu(subPage._2, path ::: subPage._1 :: Nil, false))
buffer.append(createMenu(subPage._2, path ::: subPage._1 :: Nil,
first =
false))
buffer.append("
</li>
")
}
if(page.subPages.
size > 0
) {
if(page.subPages.
nonEmpty
) {
buffer.append("
</ul>
\n")
}
buffer.toString
...
...
@@ -89,9 +89,9 @@
</button>
<ul
class=
"nav navbar-nav"
>
<li
class=
"root #if (path.
size == 0
) active #end"
>
<li
class=
"root #if (path.
isEmpty
) active #end"
>
<a
class=
"navbar-brand"
href=
"${rootPath}index.html"
>
${reportName}
#if (indexPage.subPages.
size > 0
)
<b
class=
"caret"
></b>
#end
#if (indexPage.subPages.
nonEmpty
)
<b
class=
"caret"
></b>
#end
</a>
${unescape(createMenu(indexPage))}
</li>
...
...
@@ -106,14 +106,14 @@
#if(t =
=
0)
<
li
class=
"root"
>
<a
href=
"${rootPath}index.html"
>
Home
#if (indexPage.subPages.
size > 0
)
<b
class=
"caret"
></b>
#end
#if (indexPage.subPages.
nonEmpty
)
<b
class=
"caret"
></b>
#end
</a>
${unescape(createMenu(indexPage))}
</li>
#else
<li
class=
"root #if (t == path.size) active #end"
>
<a
href=
"${rootPath}${path.slice(0,t).mkString("
",
"/",
"/")}
index.html
"
>
${path( t - 1 )}
#if (getSubPage(path.slice(0, t)).subPages.
size > 0
)
<b
class=
"caret"
></b>
#end
#if (getSubPage(path.slice(0, t)).subPages.
nonEmpty
)
<b
class=
"caret"
></b>
#end
</a>
${unescape(createMenu(getSubPage(path.slice(0, t)), path.slice(0, t)))}
</li>
...
...
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/CheckAllelesVcfInBam.scala
View file @
1ac69d32
...
...
@@ -168,9 +168,9 @@ object CheckAllelesVcfInBam extends ToolCommand {
}
for
(
allele
<-
allelesInRead
if
allele
.
length
>=
refAllele
.
length
)
{
if
(
allelesInRead
.
exists
(
(
_
.
length
)
>
allele
.
length
))
allelesInRead
-=
allele
if
(
allelesInRead
.
exists
(
_
.
length
>
allele
.
length
))
allelesInRead
-=
allele
}
if
(
allelesInRead
.
contains
(
refAllele
)
&&
allelesInRead
.
exists
(
(
_
.
length
)
<
refAllele
.
length
))
allelesInRead
-=
refAllele
if
(
allelesInRead
.
contains
(
refAllele
)
&&
allelesInRead
.
exists
(
_
.
length
<
refAllele
.
length
))
allelesInRead
-=
refAllele
if
(
allelesInRead
.
isEmpty
)
None
else
if
(
allelesInRead
.
size
==
1
)
Some
(
allelesInRead
.
head
)
else
{
...
...
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