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R3
legacy
bedtools2
Commits
33f2bef8
Commit
33f2bef8
authored
May 27, 2015
by
Aaron Quinlan
Browse files
Merge pull request #244 from nkindlon/master
Removed accidental copy in BinTree to fix speed
parents
76aa9d70
5f0362f8
Changes
5
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Inline
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src/closestFile/closestHelp.cpp
View file @
33f2bef8
...
...
@@ -73,6 +73,7 @@ void closest_help(void) {
cerr
<<
"
\t\t
For BED, the 4th column is compared."
<<
endl
<<
endl
;
IntersectCommonHelp
();
multiDbOutputHelp
();
allToolsCommonHelp
();
cerr
<<
"Notes: "
<<
endl
;
...
...
src/intersectFile/intersectHelp.cpp
View file @
33f2bef8
...
...
@@ -33,6 +33,7 @@ void intersect_help(void) {
IntersectCommonHelp
();
sortedHelp
();
multiDbOutputHelp
();
allToolsCommonHelp
();
cerr
<<
"Notes: "
<<
endl
;
...
...
src/utils/BinTree/BinTree.cpp
View file @
33f2bef8
...
...
@@ -57,17 +57,14 @@ void BinTree::getHits(Record *record, RecordKeyVector &hitSet)
return
;
}
binNumType
startBin
=
0
;
binNumType
endBin
=
0
;
binNumType
startPos
=
record
->
getStartPos
();
binNumType
endPos
=
record
->
getEndPos
();
startBin
=
(
startPos
>>
_binFirstShift
);
endBin
=
((
endPos
-
1
)
>>
_binFirstShift
);
binNumType
startBin
=
(
startPos
>>
_binFirstShift
);
binNumType
endBin
=
((
endPos
-
1
)
>>
_binFirstShift
);
const
allBinsType
bins
=
mainIter
->
second
;
const
allBinsType
&
bins
=
mainIter
->
second
;
/* SYNOPSIS:
1. We loop through each UCSC BIN level for feature A's chrom.
...
...
src/utils/general/CommonHelp.cpp
View file @
33f2bef8
...
...
@@ -69,7 +69,12 @@ void IntersectCommonHelp() {
cerr
<<
"
\t
-g
\t
"
<<
"Provide a genome file to enforce consistent chromosome sort order"
<<
endl
;
cerr
<<
"
\t\t
across input files. Only applies when used with -sorted option."
<<
endl
<<
endl
;
cerr
<<
"
\t
-nonamecheck
\t
"
<<
"For sorted data, don't throw an error if the file has different naming conventions"
<<
endl
;
cerr
<<
"
\t\t\t
for the same chromosome. ex.
\"
chr1
\"
vs
\"
chr01
\"
."
<<
endl
<<
endl
;
}
void
multiDbOutputHelp
()
{
cerr
<<
"
\t
-names
\t
"
<<
"When using multiple databases, provide an alias for each that"
<<
endl
;
cerr
<<
"
\t\t
will appear instead of a fileId when also printing the DB record."
<<
endl
<<
endl
;
...
...
@@ -78,10 +83,6 @@ void IntersectCommonHelp() {
cerr
<<
"
\t
-sortout
\t
"
<<
"When using multiple databases, sort the output DB hits"
<<
endl
;
cerr
<<
"
\t\t\t
for each record."
<<
endl
<<
endl
;
cerr
<<
"
\t
-nonamecheck
\t
"
<<
"For sorted data, don't throw an error if the file has different naming conventions"
<<
endl
;
cerr
<<
"
\t\t\t
for the same chromosome. ex.
\"
chr1
\"
vs
\"
chr01
\"
."
<<
endl
<<
endl
;
}
...
...
src/utils/general/CommonHelp.h
View file @
33f2bef8
...
...
@@ -18,5 +18,6 @@ extern void allToolsCommonHelp();
extern
void
IntersectCommonHelp
();
extern
void
IntersectOutputHelp
();
extern
void
sortedHelp
();
extern
void
multiDbOutputHelp
();
#endif
/* COMMONHELPFILE_H_ */
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