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| | == Validation Criteria Used For Reading a Sequence == | | == Validation Criteria Used For Reading a Sequence == |
| − | {| class="wikitable" style="width:100%"
| + | [[FastQ Validation Criteria]] |
| − | |+ style="font-size:150%" |'''Sequence Identifier Line'''
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| − | ! width="50%"|Validation Criteria
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| − | ! width="50%"|Error Message
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| − | |-
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| − | | Line is at least 2 characters long ('@' and at least 1 for the sequence identifier)
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| − | | ERROR on Line <current line #>: The sequence identifier line was too short.
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| − | |-
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| − | | Line starts with an '@'
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| − | | ERROR on Line <current line #>: First line of a sequence does not begin wtih @
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| − | |-
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| − | | Line does not contain a space between the '@' and the first sequence identifier (which must be at least 1 character).
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| − | | ERROR on Line <current line #>: No Sequence Identifier specified before the comment.
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| − | |-
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| − | | Every entry in the file should have a unique identifier.
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| − | | ERROR on Line <current line #>: Repeated Sequence Identifier: <identifier> at Lines <previous line #> <current line #>
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| − | |}
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| − | | |
| − | | |
| − | {| class="wikitable" style="width:100%" border="1"
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| − | |+ style="font-size:150%"|'''Raw Sequence Line'''
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| − | ! width="50%"|Validation Criteria
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| − | ! width="50%"|Error Message
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| − | |-
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| − | | A base sequence should have non-zero length.
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| − | | ERROR on Line <current line #>: Raw Sequence is shorter than the min read length: 0 < <config min read length>
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| − | |-
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| − | | All characters in the base sequence must be in the allowable set specified via configuration.
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| − | * Base Only: A C T G N a c t g n
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| − | * Color Space Only: 0 1 2 3 .(period)
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| − | | ERROR on Line <current line #>: Invalid character ('<invalid char>') in base sequence.
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| − | |-
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| − | | Reads should be of a configurable minimum length since many mappers will get into trouble with very short reads.
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| − | * If the raw sequence spans lines, the sum of the lengths of all lines are validated, not each individual line.
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| − | | ERROR on Line <current line #>: Raw Sequence is shorter than the min read length: <read length> < <config min read length>
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| − | |-
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| − | | Each Line of a Raw Sequence should have at least 1 character (not be blank).
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| − | | ERROR on Line <current line #>: Looking for continuation of Raw Sequence or '+' instead found a blank line, assuming it was part of Raw Sequence.
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| − | |}
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| − | | |
| − | | |
| − | {| class="wikitable" style="width:100%" border="1"
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| − | |+ style="font-size:150%"|'''Plus Line'''
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| − | ! width="50%"|Validation Criteria
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| − | ! width="50%"|Error Message
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| − | |-
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| − | | Must exist for every sequence.
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| − | | ERROR on Line <current line #>: Reached the end of the file without a '+' line.
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| − | |-
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| − | | If the optional sequence identifier is specified, it must equal the one on the Sequence Identifier Line.
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| − | | ERROR on Line <current line #>: Sequence Identifier on '+' line does not equal the one on the '@' line.
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| − | |}
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| − | | |
| − | | |
| − | {| class="wikitable" style="width:100%" border="1"
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| − | |+ style="font-size:150%"|'''Quality String Line'''
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| − | ! width="50%"|Validation Criteria
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| − | ! width="50%"|Error Message
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| − | |-
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| − | | A quality string should be present for every base sequence.
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| − | | ERROR on Line <current line #>: Quality string length (<quality length>) does not equal raw sequence length (<raw sequence length>)
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| − | |-
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| − | | Paired quality and base sequences should be of the same length.
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| − | | ERROR on Line <current line #>: Quality string length (<quality length>) does not equal raw sequence length (<raw sequence length>)
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| − | |-
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| − | | Valid quality values should all have ASCII codes > 32.
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| − | | ERROR on Line <current line #>: Invalid character ('<invalid char>') in quality string.
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| − | |}
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| − | | |
| | | | |
| | == Reading Sequence Assumptions == | | == Reading Sequence Assumptions == |
