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biopet.biopet
Commits
b08c67ac
Commit
b08c67ac
authored
Mar 04, 2016
by
Peter van 't Hof
Browse files
Auto style fixes
parent
a10b5ec5
Changes
1
Hide whitespace changes
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public/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/SeqStat.scala
View file @
b08c67ac
...
...
@@ -89,10 +89,10 @@ object SeqStat extends ToolCommand {
(
qual_low_boundery
<
59
,
qual_high_boundery
>
74
)
match
{
case
(
false
,
true
)
=>
phredEncoding
=
Solexa
// TODO: check this later on
// complex case, we cannot tell wheter this is a sanger or solexa
// but since the qual_high_boundery exceeds any Sanger/Illumina1.8 quals, we can `assume` this is solexa
// New @ 2016/01/26: Illumina X ten samples can contain Phred=Q42 (qual_high_boundery==75/K)
// TODO: check this later on
// complex case, we cannot tell wheter this is a sanger or solexa
// but since the qual_high_boundery exceeds any Sanger/Illumina1.8 quals, we can `assume` this is solexa
// New @ 2016/01/26: Illumina X ten samples can contain Phred=Q42 (qual_high_boundery==75/K)
case
(
true
,
true
)
=>
phredEncoding
=
Solexa
// this is definite a sanger sequence, the lower end is sanger only
case
(
true
,
false
)
=>
phredEncoding
=
Sanger
...
...
@@ -181,7 +181,7 @@ object SeqStat extends ToolCommand {
quals
++=
mutable
.
ArrayBuffer
.
fill
(
baseStats
(
pos
).
qual
.
length
-
quals
.
length
)(
0
)
}
if
(
nucs
.
length
<=
baseStats
(
pos
).
nucs
.
length
)
{
nucs
++=
mutable
.
ArrayBuffer
.
fill
(
baseStats
(
pos
).
nucs
.
length
-
nucs
.
length
)(
0
)
nucs
++=
mutable
.
ArrayBuffer
.
fill
(
baseStats
(
pos
).
nucs
.
length
-
nucs
.
length
)(
0
)
}
// count into the quals
baseStats
(
pos
).
qual
.
zipWithIndex
foreach
{
case
(
value
,
index
)
=>
quals
(
index
)
+=
value
}
...
...
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