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Véronique LEGRAND
ROCK
Commits
70c6be33
Commit
70c6be33
authored
8 years ago
by
Veronique Legrand
Browse files
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bugfix : selected reads are now written in decreasing order of quality score
parent
959bfc17
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Changes
2
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2 changed files
src/fqwriter.cpp
+2
-2
2 additions, 2 deletions
src/fqwriter.cpp
src/unit_test_fqwriter.cpp
+19
-17
19 additions, 17 deletions
src/unit_test_fqwriter.cpp
with
21 additions
and
19 deletions
src/fqwriter.cpp
+
2
−
2
View file @
70c6be33
...
@@ -20,7 +20,7 @@ using namespace std;
...
@@ -20,7 +20,7 @@ using namespace std;
// TODO this looks a little bit like getDnaStr in read_utils.cpp. Some refactoring could be useful. Think about
// TODO this looks a little bit like getDnaStr in read_utils.cpp. Some refactoring could be useful. Think about
// classes to encapsulate that without decreasing perfs.
// classes to encapsulate that without decreasing perfs.
void
writeFilteredFastq
(
FqBaseBackend
*
map_id_backend
[],
int
nb_be
,
const
srp
&
io_sr
){
void
writeFilteredFastq
(
FqBaseBackend
*
map_id_backend
[],
int
nb_be
,
const
srp
&
io_sr
){
srp
::
const_iterator
it
;
srp
::
const_
reverse_
iterator
it
;
i_dim
::
const_iterator
it_offs
;
i_dim
::
const_iterator
it_offs
;
k_dim
::
const_iterator
it_struct
;
k_dim
::
const_iterator
it_struct
;
...
@@ -35,7 +35,7 @@ void writeFilteredFastq(FqBaseBackend* map_id_backend[],int nb_be, const srp& io
...
@@ -35,7 +35,7 @@ void writeFilteredFastq(FqBaseBackend* map_id_backend[],int nb_be, const srp& io
map_id_backend
[
i
]
->
openOutputFile
();
map_id_backend
[
i
]
->
openOutputFile
();
}
}
for
(
it
=
io_sr
.
begin
();
it
!=
io_sr
.
end
();
++
it
)
{
for
(
it
=
io_sr
.
r
begin
();
it
!=
io_sr
.
r
end
();
++
it
)
{
for
(
it_offs
=
it
->
second
.
begin
();
it_offs
!=
it
->
second
.
end
();
it_offs
++
)
{
for
(
it_offs
=
it
->
second
.
begin
();
it_offs
!=
it
->
second
.
end
();
it_offs
++
)
{
unsigned
long
j
=
it_offs
->
first
;
unsigned
long
j
=
it_offs
->
first
;
for
(
it_struct
=
it_offs
->
second
.
begin
();
it_struct
!=
it_offs
->
second
.
end
();
it_struct
++
)
{
for
(
it_struct
=
it_offs
->
second
.
begin
();
it_struct
!=
it_offs
->
second
.
end
();
it_struct
++
)
{
...
...
This diff is collapsed.
Click to expand it.
src/unit_test_fqwriter.cpp
+
19
−
17
View file @
70c6be33
...
@@ -21,35 +21,37 @@ using namespace std;
...
@@ -21,35 +21,37 @@ using namespace std;
#define DEBUG
#define DEBUG
char
expected_content_PE1
[]
=
"@SRR1222430.3 3 length=236
\n
\
char
expected_content_PE1
[]
=
"@SRR1222430.1 1 length=251
\n
\
CAAACACCTGACGCGGTTCCAGCAGGTACTCCTGCACGCCAATTTCCGGGCGGGCAGTAAAGCGCTGTTTGCAGCCCGTCTGGTGCAGGCGCCCCAGATAGCGGCCAACCCATTCCATCTGATCAAGGTTATCCGCTTCGAACTGACGACCGCCAAGGCTTGGGAAAACGGCAAAGTAGAATCCCTGATGCTGATGAAGCGTGCTGTCATTAAATAAGAGCGGCGCAGCAACGGGC
\n
\
GCCCGCGAAGCGGAGCTGGCCGCCTGCAAAGGCCGTTCGCGCTCGCTGTCGCTGGATCTGTACGCCCAGTGGCGCTGCATGGAGGACAACCACGGCAAGTGGCGCTTCACCTCGCCGACCCATACCGTGCTGGCCTTCGCCCAGGCGCTGAAAGAGCTGGCGCAGGAGGGCGGCGTCAGCGCTCGCCATCAGCGCTACCGCAACAATCAGCGCCGTCTGGTGGCAGGGATGCGCGCGCTCGGCTTCCGGCC
\n
\
+SRR1222430.3 3 length=236
\n
\
+SRR1222430.1 1 length=251
\n
\
CCCCCFFCFFFFGGGGGGGGGGHHHHHFGHHHHHHHHGGGGGHHHHHGGGGGGGGGGHHHHHHGGGGGHHHHHHHHGGGGHGHGHHGGHGGGGGGGGHHHHHGGGGGHGGGGHHHHGHHHHHHHHHHHHHHHHHGGGGGGGGGGGGGGGGGGGFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFBFFFFFFFFFFFFFFFABF
\n
\
CCCCCCCCCBBCGGCGGGGG@GGGGGHHHGHBHH@GGHGGGGGGGGG@GHGHGGGHHHHHHHHHGGGGGHHHFCGGGGHHHGHHGGHHHHGGGGCCGGGGHFFGGGGGHHHHHGGGGGGCGHHHHGGGGGGGGGGGGGGGGGGAEGGFFFFFFFFFFFFFFAFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFEDFFFFFFFFFFF:DA;CCFFBBFDAFFFAFFFFFFFFA-9A>DFFFFFBFFB
\n
\
@SRR1222430.2 2 length=250
\n
\
@SRR1222430.2 2 length=250
\n
\
AGAAATTCGCCATCAGAATAAAAACCTCATATGCACATTTTCTTGTTATTGCACAGCCTGTGCCACTTTAGCGCCAGCCTCTCCGGCAATCGTGGAGAAATTAAGGAGATAGTGTAATTTATCATGTTGCTTTTGCCGTATCGTAAAGAAACCTCGAGCTTTCCTGCCAGCAGGTAGCGAGTCTGCTTCGTCACCGCAGACCGGCGCATTATCCCTTGCCGGTGTGAAACCTCATTTCATTTAAGTCAAA
\n
\
AGAAATTCGCCATCAGAATAAAAACCTCATATGCACATTTTCTTGTTATTGCACAGCCTGTGCCACTTTAGCGCCAGCCTCTCCGGCAATCGTGGAGAAATTAAGGAGATAGTGTAATTTATCATGTTGCTTTTGCCGTATCGTAAAGAAACCTCGAGCTTTCCTGCCAGCAGGTAGCGAGTCTGCTTCGTCACCGCAGACCGGCGCATTATCCCTTGCCGGTGTGAAACCTCATTTCATTTAAGTCAAA
\n
\
+SRR1222430.2 2 length=250
\n
\
+SRR1222430.2 2 length=250
\n
\
BBBBBFFFBBBBFGGGGGGGGGHHGGHHHHHHHHGFGHHHHHHHHGHHHFFFHHFHHHHHHEHGFHHHFGFGFGGGEGGFH@@HGCGGGHHGHHGGHFAFHHHEGFHHGGHHFHFHHHHHEHHHHHHHHHHHGHHHGGGGHHGHFGGFDGFGFHGEGFCDHGGHHHHHHHGHHEHHGHGGGGHGFHHEHGHGGGGDFGGGHHGADA?DBGGGGGGFFFFBBFFFFFFFFFFFFFFFFFBFFFFFFFFF/B
\n
\
BBBBBFFFBBBBFGGGGGGGGGHHGGHHHHHHHHGFGHHHHHHHHGHHHFFFHHFHHHHHHEHGFHHHFGFGFGGGEGGFH@@HGCGGGHHGHHGGHFAFHHHEGFHHGGHHFHFHHHHHEHHHHHHHHHHHGHHHGGGGHHGHFGGFDGFGFHGEGFCDHGGHHHHHHHGHHEHHGHGGGGHGFHHEHGHGGGGDFGGGHHGADA?DBGGGGGGFFFFBBFFFFFFFFFFFFFFFFFBFFFFFFFFF/B
\n
\
@SRR1222430.
3 3
length=2
36
\n
\
@SRR1222430.
1 1
length=2
51
\n
\
CAAACACCT
GA
C
GCGG
TTCC
AGC
A
GG
TACT
CCTGCA
CGCCAATTTCCGGGCGGGCAGTAAAGCGCTGTTTGCA
GCCCGT
CT
GGTGCAGG
CGCCCCAGAT
AG
C
GGCCA
A
CC
CATTCCATCTGATCAAGGT
TA
T
CCG
CTTCGAACTGACGAC
CGCC
A
AGGC
TTGGGAAAACGGCAAA
GTAG
AA
TCCC
TGATGCTGATGAAGCGTGCTGTCATTAAATAAGA
GCGGC
GCAGCAA
CGG
G
C
\n
\
GCCCGC
GA
A
GCGGAGC
T
GG
CCG
CCTGCA
AAGGCCGTTCGCGCTCGCTGTCGCTGGATCTGTAC
GCCC
A
GTGG
CGC
TGCA
T
GG
AGGACAACCACGGCA
AG
T
GGC
GCTT
CACC
TCGCCGACCCA
TACCG
TGCTGGCCTT
CGCC
C
AGGC
GCTGAAAGAGCTGGCGCAGGAGGGCGGC
GT
C
AG
CGC
TC
G
CC
ATCAGCGCTACCGCAACAATCAGCGCCGTCTGGTGGCAGGGATGC
GCG
C
GC
TCGGCTTC
CGG
C
C
\n
\
+SRR1222430.
3 3
length=2
36
\n
\
+SRR1222430.
1 1
length=2
51
\n
\
CCCCC
FFCFFFF
GGGGGGGGGGHHH
HH
F
GHHH
HHHHH
GGGGG
HHHHHGGGGGGGGGG
HHHHHHGGGGGHHHHHHHHGG
GG
H
GHG
HHGG
HGGG
GGGGGHHHHHGGGGG
HG
G
G
GHHHHG
HHHHHHHHHHHHHHHHHGGGGGGGGGGGGGGGGGGG
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
FFFFFFFFFFFFFFF
FFBFFFFFFFFF
FF
FFFF
A
BF
\n
\
CCCCC
CCCCBBCGGC
GGGGG
@
GGGGGHHHGH
B
HH
@
GG
H
GGG
GGGGGG@GHGHGGGHHH
HHHHHHGGGGGHHH
FCGGGG
HHH
G
HHGGH
H
HHGG
G
GCCGGGGHFF
GGGGGHHHHHGGGGGG
C
GHHHHG
GGGGGGGGGGGGGGGGGAEGGFFFFFFFFFFFFFFA
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
ED
FFFFFFFFFFF
:DA;CC
FFB
B
F
DAFFFA
FFFFFFFF
A-9A>D
FFFF
F
BF
FB
\n
\
"
;
"
;
char
expected_content_PE2
[]
=
"@SRR1222430.1 1 length=250
\n
\
CGATGCTGCGCTGCATCAATAAGCTGGAAGAGATCACCAGCGGCGATCTGATTGTCGATGGTCTGAAGGTCAACGACCCGAAGGTGGACGAACGTCTGATTCGTCAGGAAGCCGGGATGGTTTTCCAGCAGTTTTATCTGTTCCCGCACCTCACGGCGCTGGAAAACGTGATGTTTGGCCCGCTGCGGGTACGCGGCGCCAGCAAGCAGGCGGCGAGTGCAGGCTATCGTCGAGCAGCGGCCGGAAGCCG
\n
\
char
expected_content_PE2
[]
=
"@SRR1222430.3 3 length=236
\n
\
+SRR1222430.1 1 length=250
\n
\
GCCCGTTGCTGCGCCGCTCTTATTTAATGACAGCACGCTTCATCAGCATCAGGGATTCTACTTTGCCGTTTTCCCAAGCCTTGGCGGTCGTCAGTTCGAAGCGGATAACCTTGATCAGATGGAATGGGTTGGCCGCTATCTGGGGCGCCTGCACCAGACGGGCTGCAAACAGCGCTTTACTGCCCGCCCGGAAATTGGCGTGCAGGAGTACCTGCTGGAACCGCGTCAGGTGTTTG
\n
\
CCCCCCFFFCCCGGGGGGGGGGHHHHHHHHGHHHHHHHHHHGGGGGGGGHHGHHHHGHGHGHHHHHHHHHFHHHGGGGGGGGGGBFFHHGGGGGGHHGGHHHGHGGGHHHHHHGGGGGGGFGHGHHHHHHHHHGHHHFHHHHHHDFGGGGHHHHHGGAGGGGGGGGGGGGGGGFGGGFFFFFFFFFFFA=@FDF-BFFFFFFFFFFFFFEDFBDFFF-:FFFFFF/BFFFEFFFFFFFFFFF;--:DEFF
\n
\
+SRR1222430.3 3 length=236
\n
\
?BBABBFBBFFFGGGGGGGGGGHHHHHHHHHHFHHHGGGGGHHHHHHHGHHHHHGHGHHHHHHHGHFEGGHGHHHHHHGGHHHHHGGGEGGGHGHHHGHHGGCGGGDHHHHHHHHGHHGHGHHHHHHFHGGGHFGGGGGHHHHEFGGCFGHHHHGGFGGGGGGGGGGGGGGGGGFFFEFFFFFFFBFFFFF=;ABFF/FA:DB;BF.9.BFFFFFFF/AFFFFFABDFFB/9BD.;
\n
\
@SRR1222430.2 2 length=251
\n
\
@SRR1222430.2 2 length=251
\n
\
AGAAATTCGCCAGGGTGATCAACGTCTCATCGTCGGCGAGGGTCAGCGCCTGCGCGGGACAGTTTTCCACACAGGCCGGCCCCGCCTCGCGGCCCTGGCATAGATCGCACTTGTGCGCGCTGGCTTTCACCAGGCCTGCGGCCTGCGGCGTCACCACCACCTGCATCACCCCGAACGGGCAGGCCACCATGCAGGATTTACAGCCAATGCATTTCTCCTGACGGACCTGAACGCTGTCGCCGGACTGGGCG
\n
\
AGAAATTCGCCAGGGTGATCAACGTCTCATCGTCGGCGAGGGTCAGCGCCTGCGCGGGACAGTTTTCCACACAGGCCGGCCCCGCCTCGCGGCCCTGGCATAGATCGCACTTGTGCGCGCTGGCTTTCACCAGGCCTGCGGCCTGCGGCGTCACCACCACCTGCATCACCCCGAACGGGCAGGCCACCATGCAGGATTTACAGCCAATGCATTTCTCCTGACGGACCTGAACGCTGTCGCCGGACTGGGCG
\n
\
+SRR1222430.2 2 length=251
\n
\
+SRR1222430.2 2 length=251
\n
\
>1>AAFFF@11AEGGFFCGGGGGFGHFH2FF1F00EEE/@AEE0FGGFGEGGHGGCGC?EEFHEFEEHDF1EECHEFE/@@/BCCCFGAC@CC@C.CEGFHFHGHFHCEC?FH;CC?CG@@?-AF.BB0BFGF?E./EF;@?;AFF@<-@@??BFF?F-:A?BF999BBBF@@?@@@F-;@B@FF-A-9FF/BFFE/F//B/BBEFBFFFFF/BFFFFFFFEB?-@=B-/BBF--:;/A-B>--;>?EFE9
\n
\
>1>AAFFF@11AEGGFFCGGGGGFGHFH2FF1F00EEE/@AEE0FGGFGEGGHGGCGC?EEFHEFEEHDF1EECHEFE/@@/BCCCFGAC@CC@C.CEGFHFHGHFHCEC?FH;CC?CG@@?-AF.BB0BFGF?E./EF;@?;AFF@<-@@??BFF?F-:A?BF999BBBF@@?@@@F-;@B@FF-A-9FF/BFFE/F//B/BBEFBFFFFF/BFFFFFFFEB?-@=B-/BBF--:;/A-B>--;>?EFE9
\n
\
@SRR1222430.
3 3
length=2
36
\n
\
@SRR1222430.
1 1
length=2
50
\n
\
GCC
CG
T
TGCTGCGC
C
GCTC
TTATTTAAT
GA
C
AG
CACGCTTCATCAGCATCA
GGGAT
T
CTA
CT
TTG
C
CG
TTTTCCCAAGCCTTGGCGGTCGTCAGTTCGAAGCGGATAACCTTGATCAGATGGAATGGGTTGG
CCGCTATCTG
GGGCG
CC
T
GCACC
AG
ACGGGCTG
C
AAAC
AGCGCTT
TAC
T
GC
C
CGCC
C
GGAAATT
GGCG
T
GCAG
GAGTACCTGCTGGAACCGCGTCAGGTGTTT
G
\n
\
CG
A
TGCTGCGC
T
GC
A
TC
AATAAGCTG
GAAG
AGATCACCAGC
GG
C
GATCT
G
ATTG
T
CG
ATGGTCTGAAGGTCAACGACCCGAAGGTGGACGAACGTCTGATTCGTCAGGAAGCCGGGATGGTTTT
CC
A
GC
AGTTT
TATCTG
TTC
CCGCACC
TC
ACGG
C
GCTG
GA
AAAC
GTGATGTTTGGCCCGCTGCGGG
TACGC
GG
CGCC
AGCAAGCA
GGCGGC
G
AG
TGCAGGCTATCGTCGAGCAGCGGCCGGAAGCC
G
\n
\
+SRR1222430.
3 3
length=2
36
\n
\
+SRR1222430.
1 1
length=2
50
\n
\
?BBABBFBBFFF
GGGGGGGGGGHHHHHHHHHH
F
HHHGGGGGHHHHHH
HGHHHH
HGHGHHHHHHH
GHFEGGHGHHHH
HHGGHHH
HH
G
GGE
GGGH
G
HHH
G
HHGG
C
GGG
D
HHHHHHHHGHH
GHGH
HHHHH
FHGGGHFGGGGGHHHHEFGGCFGHHHHGGFGGGGGGGGGGGGGGGGGFFFEFFFFFFFBFFFFF=;ABFF/FA:DB;BF.9.B
FFFFFFF
/A
FFFFF
ABDFFB/9BD.;
\n
\
CCCCCCFFFCCC
GGGGGGGGGGHHHHHHHH
G
HHHHH
HHHHHGGG
GGGGGHH
G
HHHH
G
HGHGHHHHHHH
HHFHHHGGGGGGGGGGBFFHHGGGGGG
HHGGHHHG
H
GGGHHHHHHGG
GG
GGG
FGHGH
HHHHHHHHGHHH
F
HHHH
HHDFGGGGHHHHHGGAGGGGGGGGGGGGGGGFGGGFFFFFFFFFFFA=@FDF-BFFFFFFFFFFFFFEDFBD
FFF
-:
FFFF
FF/B
FFF
E
FF
FFFFFFFFF;--:DEFF
\n
\
"
;
"
;
void
test_write_PE
()
{
void
test_write_PE
()
{
srp
sr
;
srp
sr
;
srp
::
reverse_iterator
rit
;
srp
::
reverse_iterator
rit
;
...
...
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