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Michael Menzel
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Commits
5550cc84
Commit
5550cc84
authored
Nov 21, 2018
by
Michael Menzel
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Distance track support for batch analysis. Caller code and convert method
parent
26cb3628
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2
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2 changed files
with
25 additions
and
0 deletions
+25
-0
backend/src/main/java/de/thm/genomeData/tracks/Tracks.java
backend/src/main/java/de/thm/genomeData/tracks/Tracks.java
+12
-0
backend/src/main/java/de/thm/run/AnalysisHelper.java
backend/src/main/java/de/thm/run/AnalysisHelper.java
+13
-0
No files found.
backend/src/main/java/de/thm/genomeData/tracks/Tracks.java
View file @
5550cc84
...
...
@@ -26,6 +26,7 @@ import org.slf4j.LoggerFactory;
import
java.util.*
;
import
java.util.stream.Collectors
;
import
java.util.stream.DoubleStream
;
import
java.util.stream.IntStream
;
/**
* Collection of utils for track objects.
...
...
@@ -496,6 +497,17 @@ public final class Tracks {
return
TrackFactory
.
getInstance
().
createInOutTrack
(
start
,
end
,
track
.
getName
()
+
" as inout "
,
track
.
getDescription
(),
track
.
getAssembly
());
}
public
static
DistanceTrack
createDistFromInOut
(
InOutTrack
track
)
{
List
<
Long
>
midpoints
=
IntStream
.
range
(
0
,
track
.
getStarts
().
length
)
.
mapToLong
(
p
->
track
.
getEnds
()[
p
]
-
track
.
getStarts
()[
p
])
.
boxed
()
.
collect
(
Collectors
.
toList
());
return
TrackFactory
.
getInstance
().
createDistanceTrack
(
midpoints
,
"Distance from "
+
track
.
getName
(),
"Distance from "
+
track
.
getName
(),
Genome
.
Assembly
.
hg19
,
track
.
getCellLine
());
}
/**
* Returns a track created from given sites object.
...
...
backend/src/main/java/de/thm/run/AnalysisHelper.java
View file @
5550cc84
...
...
@@ -234,6 +234,19 @@ class AnalysisHelper {
logger
.
warn
(
e
.
toString
());
}
/*
//TODO Use to call create distance tracks and call for batch result histogram
// TODO build to work with hg38 -> change id's
if(packages.contains("Genetic") && command.getAssembly().equals(Genome.Assembly.hg19)){
Track cpg_distance = Tracks.createDistFromInOut((InOutTrack) TrackFactory.getInstance().getTrackByDbId(1376));
Track tss = Tracks.createDistFromInOut((InOutTrack) TrackFactory.getInstance().getTrackByDbId(1386));
tracks.add(tss);
tracks.add(cpg_distance);
}
*/
tracks
=
tracks
.
stream
().
filter
(
distinctByKey
(
Track:
:
getName
)).
collect
(
Collectors
.
toList
());
for
(
Sites
sites
:
batchSites
)
{
...
...
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