Merge pull request #44 from FitzsimmonsCM/master

Clarified error messages.
t-neumann · Jan 2, 2019 · 355169f · 355169f
2 parents c00265f + 47fb0ac
commit 355169f
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Showing 2 changed files with 2 additions and 3 deletions.
diff --git a/slamdunk/slamdunk.py b/slamdunk/slamdunk.py
@@ -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)

diff --git a/slamdunk/utils/misc.py b/slamdunk/utils/misc.py
@@ -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))