
The following parameters are available.  Ones with "[]" are in effect:

Input Parameters
 --in [testFiles/testInvalid2.bam], --noeof, --refFile [], --maxErrors [-1],
               --verbose [ON], --printableErrors [100], --disableStatistics,
               --params [ON]
   SortOrder : --so_flag, --so_coord, --so_query

1 invalid SAM/BAM Header lines were skipped due to:
SAM/BAM Header line failure: Skipping PG line that has a repeated ID field.

Record 6
INVALID_CIGAR (WARNING) : CIGAR does not evaluate to the same length as SEQ, (9 != 8).

Record 7
INVALID_CIGAR (WARNING) : CIGAR does not evaluate to the same length as SEQ, (8 != 9).


Number of records read = 10
Number of valid records = 8

Error Counts:
	INVALID_CIGAR: 2

TotalReads	10.00
MappedReads	7.00
PairedReads	10.00
ProperPair	0.00
DuplicateReads	0.00
QCFailureReads	0.00

MappingRate(%)	70.00
PairedReads(%)	100.00
ProperPair(%)	0.00
DupRate(%)	0.00
QCFailRate(%)	0.00

TotalBases	48.00
BasesInMappedReads	40.00
Returning: 7 (INVALID)
