zzh
/
gatk-3.8
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

Marginally more useful output 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3201 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
depristo 2010-04-20 14:45:14 +00:00
parent 818a95ea6e
commit 7902db616e
1 changed files with 10 additions and 2 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

12
python/Verify1KGArchiveBAMs.py
View File

@ -232,6 +232,9 @@ if __name__ == "__main__":
parser.add_option("-m", "--maxLocal", dest="maxLocalFiles",
type='int', default=None,
help="If provided, maximum number of files in the local archive to examine")
parser.add_option("-M", "--maxFiles", dest="maxFiles",
type='int', default=None,
help="If provided, maximum number of files in the local archive to examine")
parser.add_option("-q", "--quiet", dest="quiet",
action='store_true', default=False,
help="If provided, prints out the individual status of all files")
@ -262,6 +265,8 @@ if __name__ == "__main__":
compared = validateFile( file, root, ftpParsed[2] )
results[file] = compared
#localIndex
if OPTIONS.maxFiles != None and len(results) > OPTIONS.maxFiles:
break
printHeaderSep()
print 'SUMMARY: Total files examined', len(results)
@ -272,8 +277,8 @@ if __name__ == "__main__":
print 'SUMMARY: %s' % ( status )
print 'SUMMARY: Files %d (%.2f%% of total)' % ( n, n * 100.0 / len(results))
statusForFileListing = ['size-mismatch', 'local-file-missing']
maxFilesToList = 10
statusForFileListing = ['size-mismatch', 'local-file-missing', 'orphaned-file']
maxFilesToList = 20
if status in statusForFileListing:
print 'SUMMARY: listing the first', min(maxFilesToList, n), 'of', n
for file in itertools.islice(filesOfStatus, maxFilesToList):
@ -287,3 +292,6 @@ if __name__ == "__main__":
print 'SUMMARY: total size %s' % ( fileSizes )
print 'SUMMARY: last modification time %s' % ( mostRecentMod )
totalSize = MergeBAMsUtils.greek(reduce(operator.__add__, map( ComparedFiles.size, results.itervalues() )))
print '#### TOTAL PROJECT SIZE: %s' % ( totalSize )