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