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R3
legacy
bedtools2
Commits
5b00dced
Commit
5b00dced
authored
Apr 04, 2015
by
arq5x
Browse files
revcomp support for IUPAC
parent
59f252a8
Changes
1
Hide whitespace changes
Inline
Side-by-side
src/utils/sequenceUtilities/sequenceUtils.cpp
View file @
5b00dced
...
...
@@ -26,6 +26,7 @@ void reverseComplement(string &seq) {
// swap the bases
for
(
unsigned
int
i
=
0
;
i
<
seq
.
length
();
i
++
)
{
switch
(
seq
[
i
])
{
// nucleotides
case
'A'
:
seq
[
i
]
=
'T'
;
break
;
...
...
@@ -50,6 +51,94 @@ void reverseComplement(string &seq) {
case
't'
:
seq
[
i
]
=
'a'
;
break
;
// unknown (N)
case
'N'
:
seq
[
i
]
=
'N'
;
break
;
case
'n'
:
seq
[
i
]
=
'n'
;
break
;
// unknown (X)
case
'X'
:
seq
[
i
]
=
'X'
;
break
;
case
'x'
:
seq
[
i
]
=
'x'
;
break
;
// IUPAC
case
'Y'
:
seq
[
i
]
=
'R'
;
break
;
case
'y'
:
seq
[
i
]
=
'r'
;
break
;
case
'R'
:
seq
[
i
]
=
'Y'
;
break
;
case
'r'
:
seq
[
i
]
=
'y'
;
break
;
case
'S'
:
seq
[
i
]
=
'S'
;
break
;
case
's'
:
seq
[
i
]
=
's'
;
break
;
case
'W'
:
seq
[
i
]
=
'W'
;
break
;
case
'w'
:
seq
[
i
]
=
'w'
;
break
;
case
'K'
:
seq
[
i
]
=
'M'
;
break
;
case
'k'
:
seq
[
i
]
=
'm'
;
break
;
case
'M'
:
seq
[
i
]
=
'K'
;
break
;
case
'm'
:
seq
[
i
]
=
'k'
;
break
;
case
'B'
:
seq
[
i
]
=
'V'
;
break
;
case
'b'
:
seq
[
i
]
=
'v'
;
break
;
case
'V'
:
seq
[
i
]
=
'B'
;
break
;
case
'v'
:
seq
[
i
]
=
'b'
;
break
;
case
'D'
:
seq
[
i
]
=
'H'
;
break
;
case
'd'
:
seq
[
i
]
=
'h'
;
break
;
case
'H'
:
seq
[
i
]
=
'D'
;
break
;
case
'h'
:
seq
[
i
]
=
'd'
;
break
;
default:
break
;
}
...
...
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