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R3
legacy
bedtools2
Commits
070ff0d3
Commit
070ff0d3
authored
9 years ago
by
arq5x
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update the help for coverage to reflect new role of A versus B.
parent
a0778bfc
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src/coverageFile/coverageHelp.cpp
+6
-6
6 additions, 6 deletions
src/coverageFile/coverageHelp.cpp
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6 additions
and
6 deletions
src/coverageFile/coverageHelp.cpp
+
6
−
6
View file @
070ff0d3
...
...
@@ -23,14 +23,14 @@ void coverage_help(void) {
cerr
<<
"Options: "
<<
endl
;
cerr
<<
"
\t
-hist
\t
"
<<
"Report a histogram of coverage for each feature in
B
"
<<
endl
;
cerr
<<
"
\t\t
as well as a summary histogram for _all_ features in
B
."
<<
endl
<<
endl
;
cerr
<<
"
\t\t
Output (tab delimited) after each feature in
B
:"
<<
endl
;
cerr
<<
"
\t\t
1) depth
\n\t\t
2) # bases at depth
\n\t\t
3) size of
B
\n\t\t
4) % of
B
at depth"
<<
endl
<<
endl
;
cerr
<<
"
\t
-hist
\t
"
<<
"Report a histogram of coverage for each feature in
A
"
<<
endl
;
cerr
<<
"
\t\t
as well as a summary histogram for _all_ features in
A
."
<<
endl
<<
endl
;
cerr
<<
"
\t\t
Output (tab delimited) after each feature in
A
:"
<<
endl
;
cerr
<<
"
\t\t
1) depth
\n\t\t
2) # bases at depth
\n\t\t
3) size of
A
\n\t\t
4) % of
A
at depth"
<<
endl
<<
endl
;
cerr
<<
"
\t
-d
\t
"
<<
"Report the depth at each position in each
B
feature."
<<
endl
;
cerr
<<
"
\t
-d
\t
"
<<
"Report the depth at each position in each
A
feature."
<<
endl
;
cerr
<<
"
\t\t
Positions reported are one based. Each position"
<<
endl
;
cerr
<<
"
\t\t
and depth follow the complete
B
feature."
<<
endl
<<
endl
;
cerr
<<
"
\t\t
and depth follow the complete
A
feature."
<<
endl
<<
endl
;
cerr
<<
"
\t
-counts
\t
"
<<
"Only report the count of overlaps, don't compute fraction, etc."
<<
endl
<<
endl
;
...
...
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