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R3
legacy
bedtools2
Commits
702f78e2
Commit
702f78e2
authored
May 16, 2015
by
Neil Kindlon
Browse files
Fixed sample unit test
parent
ad9efaa2
Changes
2
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test/sample/sample_help_withoutVersion.txt
deleted
100644 → 0
View file @
ad9efaa2
Tool: bedtools sample (aka sampleFile)
Summary: Take sample of input file(s) using reservoir sampling algorithm.
Usage: bedtools sample [OPTIONS] -i <bed/gff/vcf/bam>
WARNING: The current sample algorithm will hold all requested sample records in memory prior to output.
The user must ensure that there is adequate memory for this.
Options:
-n The number of records to generate.
- Default = 1,000,000.
- (INTEGER)
-seed Supply an integer seed for the shuffling.
- By default, the seed is chosen automatically.
- (INTEGER)
-ubam Write uncompressed BAM output. Default writes compressed BAM.
-bed When using BAM input (-abam), write output as BED. The default
is to write output in BAM when using -abam.
-s Require same strandedness. That is, only give records
that have the same strand. Use '-s forward' or '-s reverse'
for forward or reverse strand records, respectively.
- By default, records are reported without respect to strand.
-header Print the header from the input file prior to results.
Notes:
TBD: Enter other usage notes here.
test/sample/test-sample.sh
View file @
702f78e2
...
...
@@ -30,8 +30,10 @@ $BT random -l 1000 -n 1000 -g human.hg19.genome >> mainFile.bed
# Test that help is printed when no args are given
############################################################
echo
" sample.t01...
\c
"
$BT
sample 2>&1
>
/dev/null |
grep
-iv
version
>
obs
check obs sample_help_withoutVersion.txt
echo
\
"***** ERROR: No input file given. Exiting. *****"
>
exp
$BT
sample 2>&1
>
/dev/null |
head
-2
|
tail
-1
>
obs
check obs exp
rm
obs
...
...
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