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ORG.Asm
ORG.Asm
Commits
54380dbf
Commit
54380dbf
authored
Feb 18, 2014
by
Eric Coissac
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14 changed files
with
165 additions
and
46 deletions
+165
-46
orgasm-1.py
python/orgasm-1.py
+8
-2
tango.py
python/orgasm/tango.py
+123
-25
version.py
python/orgasm/version.py
+5
-0
sandbox.py
python/sandbox.py
+0
-0
buildcode.c
src/buildcode.c
+1
-1
buildcomplement.c
src/buildcomplement.c
+1
-1
buildindex.c
src/buildindex.c
+1
-1
compsort.c
src/compsort.c
+4
-4
decode.c
src/decode.c
+7
-7
fastq.c
src/fastq.c
+2
-2
load.c
src/load.c
+1
-1
lookfor.c
src/lookfor.c
+2
-2
orgasm.h
src/orgasm.h
+6
-0
orgasmi.c
src/orgasmi.c
+4
-0
No files found.
python/orgasm-1.py
View file @
54380dbf
...
...
@@ -5,11 +5,17 @@
# ./orgasm/build/lib.macosx-10.6-intel-2.7/
# python orgasm-1.py GWM-261 COX1.fasta
from
orgasm.tango
import
tango
,
matchtoseed
,
cutLowCoverage
,
scaffold
,
coverageEstimate
from
orgasm.tango
import
tango
,
\
matchtoseed
,
\
cutLowCoverage
,
\
scaffold
,
\
coverageEstimate
,
\
insertFragment
from
orgasm.indexer
import
_orgasm
as
indexer
from
orgasm.backtranslate.fasta
import
fasta
from
orgasm.assembler
import
Assembler
from
orgasm.multialign
import
multiAlignReads
,
\
consensus
import
sys
if
__name__
==
'__main__'
:
...
...
python/orgasm/tango.py
View file @
54380dbf
This diff is collapsed.
Click to expand it.
python/orgasm/version.py
0 → 100644
View file @
54380dbf
major
=
0
minor
=
0
serial
=
'alpha'
version
=
"
%2
d.
%02
d
%
s"
%
(
major
,
minor
,
serial
)
python/sandbox.py
View file @
54380dbf
This diff is collapsed.
Click to expand it.
src/buildcode.c
View file @
54380dbf
...
...
@@ -14,7 +14,7 @@ int main(int argc, char *argv[])
uint32_t
icode
;
char
nuc
[
9
];
int
i
;
uint16_t
mask
;
//
uint16_t mask;
nuc
[
8
]
=
0
;
...
...
src/buildcomplement.c
View file @
54380dbf
...
...
@@ -18,7 +18,7 @@ int main(int argc, char *argv[])
char
cnuc
[
5
];
int
i
;
uint16_t
mask
;
//
uint16_t mask;
nuc
[
4
]
=
0
;
cnuc
[
4
]
=
0
;
...
...
src/buildindex.c
View file @
54380dbf
...
...
@@ -21,7 +21,7 @@ buffer_t *buildIndex(const char *forwardFileName, const char* reverseFileName,
char
*
indexFileName
;
// uint32_t indexcount;
uint32_t
i
;
//
uint32_t i;
buffer_t
*
reads
;
forward
=
fopen
(
forwardFileName
,
"r"
);
...
...
src/compsort.c
View file @
54380dbf
...
...
@@ -38,14 +38,14 @@ void partialCompSortBuffer(buffer_t *buffer,
uint8_t
word
;
uint32_t
i
;
uint32_t
swap
;
uint32_t
pairswap
;
//
uint32_t pairswap;
uint32_t
next
;
uint32_t
first
;
uint32_t
pair
;
uint32_t
*
pairp
;
//
uint32_t pair;
//
uint32_t *pairp;
uint32_t
*
swapp
;
uint32_t
cumsum
=
start
;
uint32_t
backtolastswap
=
FALSE
;
//
uint32_t backtolastswap=FALSE;
int32_t
shiftmax
=
0
;
if
(
shift
>
shiftmax
)
shiftmax
=
shift
;
...
...
src/decode.c
View file @
54380dbf
...
...
@@ -34,13 +34,13 @@ char * decode(buffer_t *buffer, uint32_t recordid, uint32_t begin, int32_t lengt
uint32_t
shift
;
uint32_t
i
;
uint32_t
lcompact
;
uint32_t
mask
;
//
uint32_t mask;
uint16_t
*
compactseq
;
if
(
dest
==
NULL
)
dest
=
internal
;
dest
=
(
char
*
)
PTR8
(
dest
);
idest
=
(
uint
16
_t
*
)
dest
;
idest
=
(
uint
64
_t
*
)
dest
;
from
=
recordid
*
buffer
->
recordSize
+
((
begin
>>
2
)
&
0xFFFFFFFE
);
shift
=
begin
&
7
;
...
...
@@ -66,7 +66,7 @@ char *decodeComp(buffer_t *buffer, uint32_t recordid, uint32_t begin, int32_t le
uint32_t
shift
;
int32_t
i
;
uint32_t
lcompact
;
uint32_t
mask
;
//
uint32_t mask;
uint16_t
*
compactseq
;
size_t
lkey
;
char
*
key
;
...
...
@@ -76,7 +76,7 @@ char *decodeComp(buffer_t *buffer, uint32_t recordid, uint32_t begin, int32_t le
dest
=
(
char
*
)
PTR8
(
dest
);
dest2
=
(
char
*
)
PTR8
(
internal2
);
idest
=
(
uint
16
_t
*
)
dest
;
idest
=
(
uint
64
_t
*
)
dest
;
from
=
buffer
->
readSize
-
begin
;
...
...
@@ -103,7 +103,7 @@ char *decodeComp(buffer_t *buffer, uint32_t recordid, uint32_t begin, int32_t le
shift
=
(
4
-
(
from
&
3
))
&
3
;
ASSERT
(
shift
<
4
,
"There is a bug readsize = %
d
begin = %d shift=%d"
,
buffer
->
readSize
,
begin
,
shift
)
ASSERT
(
shift
<
4
,
"There is a bug readsize = %
zu
begin = %d shift=%d"
,
buffer
->
readSize
,
begin
,
shift
)
lcompact
=
(
length
+
shift
)
/
8
+
(((
length
+
shift
)
&
7
)
?
1
:
0
);
...
...
@@ -149,13 +149,13 @@ char * decodeSequence(pnuc buffer, uint32_t begin, int32_t length, char *dest)
uint32_t
shift
;
uint32_t
i
;
uint32_t
lcompact
;
uint32_t
mask
;
//
uint32_t mask;
uint16_t
*
compactseq
;
if
(
dest
==
NULL
)
dest
=
internal
;
dest
=
(
char
*
)
PTR8
(
dest
);
idest
=
(
uint
16
_t
*
)
dest
;
idest
=
(
uint
64
_t
*
)
dest
;
from
=
((
begin
>>
2
)
&
0xFFFFFFFE
);
shift
=
begin
&
7
;
...
...
src/fastq.c
View file @
54380dbf
...
...
@@ -204,7 +204,7 @@ buffer_t * loadPairedFastq(FILE* forward,
char
*
bufferend
;
// uint32_t readLength;
uint32_t
recordLength
;
uint32_t
nextprint
;
uint32_t
nextprint
=
0
;
uint32_t
*
encodedseqs
;
buffer_t
*
seqbuffer
;
...
...
@@ -227,7 +227,7 @@ buffer_t * loadPairedFastq(FILE* forward,
seqbuffer
=
newBuffer
(
maxbuffersize
,
readLength
,
maxread
);
encodedseqs
=
(
uint32_t
*
)(
seqbuffer
->
records
);
printf
(
"maximum reads : %
d
\n
"
,
seqbuffer
->
maxrecord
);
printf
(
"maximum reads : %
zu
\n
"
,
seqbuffer
->
maxrecord
);
while
(
readLength
&&
(
seqbuffer
->
readCount
+
2
)
<=
seqbuffer
->
maxrecord
)
...
...
src/load.c
View file @
54380dbf
...
...
@@ -14,7 +14,7 @@ void indexReverseComplement(buffer_t *reads)
if
(
reads
->
complement
)
FREE
(
reads
->
complement
);
reads
->
complement
=
(
int32_t
*
)
MALLOC
(
sizeof
(
int32_t
)
*
reads
->
readCount
);
reads
->
complement
=
(
uint32_t
*
)
MALLOC
(
sizeof
(
u
int32_t
)
*
reads
->
readCount
);
for
(
i
=
0
;
i
<
reads
->
readCount
;
i
++
)
reads
->
complement
[
reads
->
order1
[
i
]]
=
i
;
...
...
src/lookfor.c
View file @
54380dbf
...
...
@@ -249,7 +249,7 @@ int32_t lookForForward(buffer_t *buffer, pnuc key, size_t length, int32_t* endof
int32_t
end
;
int32_t
middle
;
int32_t
comp
;
int32_t
comp1
;
//
int32_t comp1;
// I set the end of list flag to 0
*
endoflist
=
0
;
...
...
@@ -436,7 +436,7 @@ int32_t lookForReverse(buffer_t *buffer, pnuc key, size_t length, int32_t* endof
int32_t
nextReverse
(
buffer_t
*
buffer
,
int32_t
current
,
size_t
length
,
int32_t
*
endoflist
)
{
int32_t
pos
=
current
+
1
;
int32_t
lkey
=
CODELENGTH
(
buffer
->
readSize
);
//
int32_t lkey = CODELENGTH(buffer->readSize);
pnuc
key
=
(
pnuc
)((
uint8_t
*
)(
buffer
->
records
)
+
buffer
->
recordSize
*
buffer
->
order1
[
current
]);
int32_t
rshift
=
buffer
->
readSize
&
3
;
int
comp
=
cmpCompPrefix
(
buffer
,
buffer
->
order1
[
pos
],
key
,
length
+
((
rshift
==
0
)
?
0
:
(
4
-
rshift
)));
...
...
src/orgasm.h
View file @
54380dbf
...
...
@@ -132,6 +132,8 @@ void writeGeneralData(buffer_t *buffer,FILE* output);
void
loadSequences
(
buffer_t
*
buffer
,
FILE
*
input
);
void
loadPairData
(
buffer_t
*
buffer
,
FILE
*
input
);
void
loadGeneralData
(
buffer_t
*
buffer
,
FILE
*
input
);
uint32_t
loadOrder1
(
buffer_t
*
buffer
,
FILE
*
input
);
void
fillOrdored
(
buffer_t
*
buffer
);
void
sortBuffer
(
buffer_t
*
buffer
);
...
...
@@ -162,5 +164,9 @@ extern uint32_t expanded8bitsnuc[];
pnuc
encodeSequence
(
pnuc
dest
,
char
*
src
,
uint32_t
length
);
pnuc
shiftKey
(
pnuc
dest
,
pnuc
key
,
uint32_t
shift
,
uint32_t
keyLength
);
void
countLetterAt
(
buffer_t
*
buffer
,
uint32_t
pos
);
uint32_t
minSuffix
(
buffer_t
*
buffer
,
uint32_t
pos
);
#endif
/* ORGASM_H_ */
src/orgasmi.c
View file @
54380dbf
...
...
@@ -143,7 +143,11 @@ if ((argc -= optind) == 2)
strcpy
(
reverseFileName
,
argv
[
optind
]);
}
else
{
errflag
++
;
forwardFileName
=
NULL
;
reverseFileName
=
NULL
;
}
if
(
indexfiles
==
NULL
)
...
...
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