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
39bcb468
Commit
39bcb468
authored
Mar 09, 2015
by
bow
Browse files
Merge branch 'patch-seqstat' into 'develop'
Patch seqstat Fix for #121 See merge request !119
parents
5d854a9f
bd8f8477
Changes
1
Hide whitespace changes
Inline
Side-by-side
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/Seqstat.scala
View file @
39bcb468
...
...
@@ -164,14 +164,11 @@ object Seqstat extends ToolCommand {
case
class
ReadStat
(
qual
:
mutable.ArrayBuffer
[
Long
]
=
mutable
.
ArrayBuffer
(),
nuc
:
mutable.ArrayBuffer
[
Long
]
=
mutable
.
ArrayBuffer
.
fill
(
'T'
.
toInt
+
1
)(
0
),
var
withN
:
Long
,
var
withN
:
Long
=
0L
,
lengths
:
mutable.ArrayBuffer
[
Int
]
=
mutable
.
ArrayBuffer
())
val
baseStats
:
mutable.ArrayBuffer
[
BaseStat
]
=
mutable
.
ArrayBuffer
()
val
readStats
:
ReadStat
=
new
ReadStat
(
mutable
.
ArrayBuffer
(),
mutable
.
ArrayBuffer
.
fill
(
'T'
.
toInt
+
1
)(
0
),
0L
,
mutable
.
ArrayBuffer
())
val
readStats
:
ReadStat
=
new
ReadStat
()
/**
* Compute the quality metric per read
...
...
@@ -194,6 +191,9 @@ object Seqstat extends ToolCommand {
val
readQual
=
record
.
getBaseQualityString
val
readNucleotides
=
record
.
getReadString
if
(
record
.
length
>=
readStats
.
lengths
.
size
)
// Extends array when length not yet possible
(
0
to
(
record
.
length
-
readStats
.
lengths
.
size
)).
foreach
(
_
=>
readStats
.
lengths
.
append
(
0
))
readStats
.
lengths
(
record
.
length
)
+=
1
for
(
t
<-
0
until
record
.
length
())
{
...
...
@@ -211,10 +211,7 @@ object Seqstat extends ToolCommand {
readStats
.
qual
++=
mutable
.
ArrayBuffer
.
fill
(
avgQual
-
readStats
.
qual
.
length
+
1
)(
0
)
}
readStats
.
qual
(
avgQual
)
+=
1
readStats
.
withN
+=
{
if
(
readNucleotides
.
contains
(
"N"
))
1L
else
0L
}
if
(
readNucleotides
.
contains
(
"N"
))
readStats
.
withN
+=
1L
}
/**
...
...
@@ -278,7 +275,7 @@ object Seqstat extends ToolCommand {
}
for
(
pos
<-
0
until
readStats
.
qual
.
length
)
{
va
r
key
:
Int
=
pos
-
phredEncoding
.
id
va
l
key
:
Int
=
pos
-
phredEncoding
.
id
if
(
key
>
0
)
{
// count till the max of baseHistogram.length
for
(
histokey
<-
0
until
key
+
1
)
{
...
...
@@ -319,7 +316,7 @@ object Seqstat extends ToolCommand {
),
(
"stats"
,
Map
(
(
"bases"
,
Map
(
(
"num_n"
,
nucleotideHistoMap
(
'N'
)),
(
"num_n"
,
nucleotideHistoMap
.
getOrElse
(
'N'
,
0
)),
(
"num_total"
,
nucleotideHistoMap
.
values
.
sum
),
(
"num_qual_gte"
,
baseQualHistoMap
.
toMap
),
(
"nucleotides"
,
nucleotideHistoMap
.
toMap
)
...
...
@@ -335,9 +332,6 @@ object Seqstat extends ToolCommand {
))
)
val
jsonReport
:
Json
=
{
ConfigUtils
.
mapToJson
(
report
)
}
println
(
jsonReport
.
spaces2
)
println
(
ConfigUtils
.
mapToJson
(
report
).
spaces2
)
}
}
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