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Clarified error messages. #44

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merged 1 commit into from
Jan 2, 2019
Merged

Clarified error messages. #44

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2 changes: 1 addition & 1 deletion slamdunk/slamdunk.py
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Original file line number Diff line number Diff line change
Expand Up @@ -188,7 +188,7 @@ def runCount(tid, bam, ref, bed, maxLength, minQual, conversionThreshold, output
if (maxLength == None) :
maxLength = estimateMaxReadLength(bam)
if (maxLength < 0) :
print("Could not reliable estimate maximum read length. Please specify --max-read-length parameter.")
print("Difference between minimum and maximum read length is > 10. Please specify --max-read-length parameter.")
sys.exit(0)

log = getLogFile(outputLOG)
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3 changes: 1 addition & 2 deletions slamdunk/utils/misc.py
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Expand Up @@ -146,8 +146,7 @@ def removeFile(files):

def checkStep(inFiles, outFiles, force=False):
if not files_exist(inFiles):
print(inFiles, outFiles)
raise RuntimeError("One or more input files don't exist.")
raise RuntimeError("One or more input files don't exist: " + str(inFiles))
inFileDate = os.path.getmtime(inFiles[0])
for x in inFiles[1:]:
inFileDate = max(inFileDate, os.path.getmtime(x))
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