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

Input Parameters
 --in [testFiles/testInvalid.sam], --noeof,
               --refFile [testFilesLibBam/chr1_partial.fa], --maxErrors [-1],
               --verbose [ON], --printableErrors [100], --disableStatistics,
               --params [ON]
   SortOrder : --so_flag, --so_coord, --so_query

Record 1
INVALID_QNAME (ERROR) : Invalid Query Name - the string length (256) does not match the specified query name length (0).
INVALID_QNAME (WARNING) : Invalid Query Name (QNAME) length: 256.  Length with the terminating null must be between 2 & 255.
INVALID_TAG (WARNING) : Incorrect MD Tag, 37, should be NNNNN^NN0.

Record 2
INVALID: 0 length Query Name.

Record 3
INVALID_QNAME (WARNING) : Invalid character in the Query Name (QNAME): ' ' at position 2.
INVALID_TAG (WARNING) : Incorrect MD Tag, 30A0C5, should be 2T1N0.

Record 4
FAIL_PARSE: flag, 29M5I3M:F:295, is not an integer.
FAIL_PARSE: Invalid Tag Format: *, should be cc:c:x*.

Record 5
FAIL_PARSE: Too few columns (1) in the Record, expected at least 11.

Record 6
INVALID_TAG (WARNING) : Incorrect MD Tag, 30A0C5, should be UNKNOWN.

Record 7
FAIL_PARSE: flag, 9K7, is not an integer.

Record 8
FAIL_PARSE: flag, , is not an integer.

Record 10
FAIL_PARSE: flag, 65536, is not between 0 and (2^16)-1 = 65535.

Record 11
FAIL_PARSE: flag, -1, is not between 0 and (2^16)-1 = 65535.

Record 12
INVALID_RNAME (WARNING) : RNAME, rn ame, was not found in a SAM Header SQ record
INVALID_RNAME (WARNING) : Invalid character in the Reference Sequence Name (RNAME): ' ' at position 2.

Record 13
INVALID_RNAME (WARNING) : RNAME, rna@me, was not found in a SAM Header SQ record
INVALID_RNAME (WARNING) : Invalid character in the Reference Sequence Name (RNAME): '@' at position 3.

Record 14
INVALID_RNAME (WARNING) : RNAME, rnam=e, was not found in a SAM Header SQ record
INVALID_RNAME (WARNING) : Invalid character in the Reference Sequence Name (RNAME): '=' at position 4.

Record 15
FAIL_PARSE: position, ame, is not an integer.
FAIL_PARSE: mate position, *, is not an integer.
FAIL_PARSE: Invalid Tag Format: *, should be cc:c:x*.

Record 16
FAIL_PARSE: Too few columns (3) in the Record, expected at least 11.

Record 17
FAIL_PARSE: Too few columns (9) in the Record, expected at least 11.

Record 18
INVALID_RNAME (WARNING) : RNAME, , was not found in a SAM Header SQ record
INVALID_RNAME (WARNING) : Reference Sequence Name (RNAME) cannot have 0 length.

Record 19
FAIL_PARSE: position, , is not an integer.

Record 20
INVALID_POS (WARNING) : POS out of range (536870912) must be between 0 and (2^29)-1.

Record 21
INVALID_POS (WARNING) : POS out of range (-1) must be between 0 and (2^29)-1.

Record 22
FAIL_PARSE: position, 2147483648, does not fit in a 32 bit signed int.

Record 23
FAIL_PARSE: position, -2147483649, does not fit in a 32 bit signed int.

Record 24
FAIL_PARSE: position, 12r2, is not an integer.

Record 25
FAIL_PARSE: map quality, 12r2, is not an integer.

Record 26
FAIL_PARSE: map quality, , is not an integer.

Record 27
FAIL_PARSE: map quality, 256, is not between 0 and (2^8)-1 = 255.

Record 28
FAIL_PARSE: map quality, -1, is not between 0 and (2^8)-1 = 255.

Record 29
INVALID_QUAL (WARNING) : QUAL is not the same length as SEQ, (5 != 4).

Record 30
INVALID_QUAL (WARNING) : QUAL is not the same length as SEQ, (3 != 4).

Record 31
INVALID_CIGAR (WARNING) : CIGAR does not evaluate to the same length as SEQ, (5 != 4).

Record 32
INVALID_CIGAR (WARNING) : CIGAR does not evaluate to the same length as SEQ, (3 != 4).


Number of records read = 32
Number of valid records = 1

Error Counts:
	FAIL_PARSE: 17
	INVALID: 1
	INVALID_QNAME: 3
	INVALID_RNAME: 8
	INVALID_POS: 2
	INVALID_CIGAR: 2
	INVALID_QUAL: 2
	INVALID_TAG: 3

TotalReads	14.00
MappedReads	14.00
PairedReads	6.00
ProperPair	0.00
DuplicateReads	0.00
QCFailureReads	0.00

MappingRate(%)	100.00
PairedReads(%)	42.86
ProperPair(%)	0.00
DupRate(%)	0.00
QCFailRate(%)	0.00

TotalBases	47.00
BasesInMappedReads	47.00
Returning: 7 (INVALID)
