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minerva
core
Commits
5a088347
Commit
5a088347
authored
Sep 27, 2021
by
Piotr Gawron
Browse files
always show gentic data overlays
parent
375a3081
Pipeline
#47688
passed with stage
in 18 minutes and 10 seconds
Changes
2
Pipelines
1
Hide whitespace changes
Inline
Side-by-side
CHANGELOG
View file @
5a088347
minerva
(
16.0.0
~
beta
.3
)
stable
;
urgency
=
medium
*
Bug
fix
:
show
genetic
data
overlays
in
InfoWindow
even
when
no
data
is
available
(#
1562
)
*
Bug
fix
:
speed
of
opening
map
is
improved
(#
1558
)
*
Bug
fix
:
typo
(#
1555
)
*
Bug
fix
:
gene
mapping
with
empty
url
caused
issues
when
opening
info
window
...
...
@@ -8,7 +10,7 @@ minerva (16.0.0~beta.3) stable; urgency=medium
*
Bug
fix
:
sometimes
wrong
icn
numbers
were
attached
to
search
results
(#
1556
)
--
Piotr
Gawron
<
piotr
.
gawron
@
uni
.
lu
>
Mon
,
27
Sep
2021
08
:
00
:
00
+
0200
--
Piotr
Gawron
<
piotr
.
gawron
@
uni
.
lu
>
Mon
,
27
Sep
2021
14
:
00
:
00
+
0200
minerva
(
16.0.0
~
beta
.2
)
stable
;
urgency
=
medium
*
Small
improvement
:
backgrounds
are
separated
from
general
overlays
(#
1532
)
...
...
frontend-js/src/main/js/map/window/AliasInfoWindow.js
View file @
5a088347
...
...
@@ -366,6 +366,12 @@ AliasInfoWindow.prototype.adjustPileupRangeVisibility = function (pileupRange) {
pileupRange
.
stop
+=
Math
.
ceil
((
50
-
dist
)
/
2
);
}
if
(
pileupRange
.
stop
<
pileupRange
.
start
)
{
var
tmp
=
pileupRange
.
stop
;
pileupRange
.
stop
=
pileupRange
.
start
;
pileupRange
.
start
=
tmp
;
}
if
(
pileupRange
.
start
<
0
)
{
pileupRange
.
stop
-=
pileupRange
.
start
;
pileupRange
.
start
=
0
;
...
...
@@ -414,8 +420,12 @@ AliasInfoWindow.prototype.createGenomicDiv = function (params) {
var
promises
=
[];
var
overlaysData
=
[];
overlays
.
forEach
(
function
(
overlay
)
{
var
overlayGeneticInformation
=
[];
overlays
.
forEach
(
function
(
overlay
,
index
)
{
promises
.
push
(
overlay
.
getFullAliasesById
(
self
.
getAlias
().
getId
()));
globalGeneVariants
[
index
]
=
[];
overlayGeneticInformation
[
index
]
=
(
overlay
.
getType
()
===
LayoutAlias
.
GENETIC_VARIANT
);
if
(
overlay
.
getType
()
===
LayoutAlias
.
GENETIC_VARIANT
)
{
geneticInformation
=
true
;
promises
.
push
(
self
.
getCustomMap
().
getTopMap
().
getReferenceGenome
(
overlay
.
getGenomeType
(),
...
...
@@ -429,7 +439,7 @@ AliasInfoWindow.prototype.createGenomicDiv = function (params) {
logger
.
warn
(
"
Genome for
"
+
overlay
.
getGenomeType
()
+
"
,
"
+
overlay
.
getGenomeVersion
()
+
"
not loaded
"
);
}
}
,
function
()
{
}
).
catch
(
function
()
{
logger
.
warn
(
"
Genome for
"
+
overlay
.
getGenomeType
()
+
"
,
"
+
overlay
.
getGenomeVersion
()
+
"
not loaded
"
);
...
...
@@ -472,7 +482,6 @@ AliasInfoWindow.prototype.createGenomicDiv = function (params) {
}
for
(
i
=
0
;
i
<
overlaysData
.
length
;
i
++
)
{
var
data
=
overlaysData
[
i
];
globalGeneVariants
[
i
]
=
[];
if
(
data
!==
null
&&
data
!==
undefined
&&
data
.
getType
()
===
LayoutAlias
.
GENETIC_VARIANT
)
{
var
geneVariants
=
data
.
getGeneVariants
();
for
(
var
j
=
0
;
j
<
geneVariants
.
length
;
j
++
)
{
...
...
@@ -495,9 +504,12 @@ AliasInfoWindow.prototype.createGenomicDiv = function (params) {
contentElement
.
innerHTML
=
"
No reference genome defined for this MINERVA instance, cannot display variant data.
"
;
}
}
else
{
for
(
i
=
0
;
i
<
overlaysData
.
length
;
i
++
)
{
if
(
globalGeneVariants
[
i
].
length
>
0
)
{
var
vcfContent
=
self
.
createVcfString
(
globalGeneVariants
[
i
]);
for
(
i
=
0
;
i
<
overlays
.
length
;
i
++
)
{
var
vcfContent
=
undefined
;
if
(
overlayGeneticInformation
[
i
])
{
vcfContent
=
self
.
createVcfString
(
globalGeneVariants
[
i
]);
}
if
(
vcfContent
!==
undefined
)
{
pileupSource
.
push
({
viz
:
pileup
.
viz
.
variants
(),
data
:
pileup
.
formats
.
vcf
({
...
...
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