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Aborts if the specified file could not be opened.
Aborts if the specified file could not be opened.
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== Statistics ==
=== Statistic Generation ===
The statistics only reflect alignments that were successfully read from the BAM file. Alignments that failed to parse from the file are not reflected in the statistics, but alignments that are invalid for other reasons may show up in the statistics.
The following Statistics are generated by the BAM Validator if the <code>--disableStatistics</code> option is not set:
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|+ '''Read Counts'''
! Statistic !! Description
|-
|TotalReads
| Total number of alignments that were successfully read from the file.
|-
|MappedReads
| Total number of alignments that were successfully read from the file with FLAG bit 0x004 set to 0 (not unmapped).
|-
|PairedReads
| Total number of alignments that were successfully read from the file with FLAG bit 0x001 set to 1 (paired).
|-
|ProperPair
| Total number of alignments that were successfully read from the file with FLAG bits 0x001 set to 1 (paired) AND 0x002 (proper pair).
|-
|DuplicateReads
| Total number of alignments that were successfully read from the file with FLAG bit 0x400 set to 1 (PCR or optical duplicate).
|-
|QCFailureReads
| Total number of alignments that were successfully read from the file with FLAG bit 0x200 set to 1 (failed quality checks).
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|- '''Read Percentages'''
! Statistic !! Description
|-
|MappingRate(%)
| 100 * MappedReads/TotalReads
|-
|PairedReads(%)
| 100 * PairedReads/TotalReads
|-
|ProperPair(%)
| 100 * ProperPair/TotalReads
|-
|DupRate(%)
| 100 * DuplicateReads/TotalReads
|-
|QCFailRate(%)
| 100 * QCFailureReads/TotalReads
|}
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|- '''Base Counts'''
! Statistic !! Description
|-
|TotalBases
| Sum of the SEQ lengths for all alignments that were successfully read from the file.
|-
|BasesInMappedReads
| Sum of the SEQ lengths for all alignments that were successfully read from the file with FLAG bit 0x004 set to 0 (not unmapped).
|}
NOTE: If the TotalReads is greater than 10^6, then the Read Counts and Base Counts specify the total counts divided by 10^6. This is indicated in the output with a (e6) appended to the field name.
== Usage Examples ==
== Usage Examples ==
[[Sam Library Usage Examples]]
[[Sam Library Usage Examples]]
