Nothing
test.calculateTargetLength <- function(){
config.filename <- "test-data/test_config.txt"
save.dir <- setupTestFramework(config.filename=config.filename, testname="test.calcTargetLengths")
bam.file <- getPackageFile("test-data/bam_files_unit_test_PE/test_pe.gsnap.merged.concordant_uniq.bam")
observed.table = calculateTargetLengths(bam.file, save.dir)
## repeat 2 times, to simulate paired reads
isizes.from.bam <- rep(c(822,
15949,
188,
1016,
250,
233,
190,
9927,
25527,
234,
250,
338,
11181,
220), 2)
expected.summary <- summary(abs(isizes.from.bam))
checkTrue(all(observed.table['Full_Data_Set'] == expected.summary),
'calculateTargetLength() computes correct summary')
## we trust summary() to do its jobs, so only test that we get something back that looks like summary output
checkEquals(names(observed.table), c('Trimmed_Data_Set', 'Full_Data_Set'),
"calculateTargetLengths() returns summary table")
checkTrue(file.exists(file.path(save.dir,'reports','images','TargetLengths.pdf')),
'calculateTargetLengths() writes pdf')
checkTrue(file.exists(file.path(save.dir,'reports','images','TargetLengths.png')),
'calculateTargetLengths() writes png')
}
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