Commit 702f78e2 authored by Neil Kindlon's avatar Neil Kindlon
Browse files

Fixed sample unit test

parent 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.
......@@ -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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