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R3
legacy
bedtools2
Commits
c795f08e
Commit
c795f08e
authored
15 years ago
by
Aaron
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Updated the help message for fastaFromBed
- Added the -name parameter. It was missing, so users had no idea it existed.
parent
400b35b6
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1 changed file
src/fastaFromBed/fastaFromBedMain.cpp
+4
-3
4 additions, 3 deletions
src/fastaFromBed/fastaFromBedMain.cpp
with
4 additions
and
3 deletions
src/fastaFromBed/fastaFromBedMain.cpp
+
4
−
3
View file @
c795f08e
...
...
@@ -83,8 +83,6 @@ int main(int argc, char* argv[]) {
Bed2Fa
*
b2f
=
new
Bed2Fa
(
useNameOnly
,
fastaDbFile
,
bedFile
,
fastaOutFile
);
b2f
->
ExtractDNA
();
cerr
<<
PROGRAM_NAME
<<
" completed."
<<
endl
;
return
0
;
}
else
{
...
...
@@ -101,7 +99,7 @@ void ShowHelp(void) {
cerr
<<
"==============================================="
<<
endl
<<
endl
;
cerr
<<
"Description: Extract DNA sequences into a fasta file based on BED coordinates."
<<
endl
<<
endl
;
cerr
<<
"Usage: "
<<
PROGRAM_NAME
<<
" -db
<fasta db file> -bed <bed coordinates file> -fo <output fasta file w/ requested DNA>
"
<<
endl
<<
endl
;
cerr
<<
"Usage: "
<<
PROGRAM_NAME
<<
" -db
-bed -fo -name
"
<<
endl
<<
endl
;
cerr
<<
"Input Files:"
<<
endl
;
cerr
<<
" -db <FASTA db file> "
<<
endl
;
...
...
@@ -110,6 +108,9 @@ void ShowHelp(void) {
cerr
<<
"Output Files:"
<<
endl
;
cerr
<<
" -fo <FASTA output file> "
<<
endl
;
cerr
<<
"Options:"
<<
endl
;
cerr
<<
" -name Use the BED name field (#4) for the FASTA header "
<<
endl
;
cerr
<<
"
\n
Help:"
<<
endl
;
cerr
<<
" -h shows this help text"
<<
endl
;
...
...
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