Line 7: |
Line 7: |
| |- | | |- |
| | Line is at least 2 characters long ('@' and at least 1 for the sequence identifier) | | | Line is at least 2 characters long ('@' and at least 1 for the sequence identifier) |
− | | ERROR on Line <current line #>: | + | | ERROR on Line <current line #>: The sequence identifier line was too short. |
| |- | | |- |
| | Line starts with an '@' | | | Line starts with an '@' |
− | | ERROR on Line <current line #>: | + | | 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). | | | 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 #>: | + | | ERROR on Line <current line #>: No Sequence Identifier specified before the comment. |
| |- | | |- |
| | Every entry in the file should have a unique identifier. | | | Every entry in the file should have a unique identifier. |
Line 26: |
Line 26: |
| |- | | |- |
| | A base sequence should have non-zero length. | | | A base sequence should have non-zero length. |
− | | ERROR on Line <current line #>: | + | | 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. | | | All characters in the base sequence must be in the allowable set specified via configuration. |
Line 32: |
Line 32: |
| * Color Space Only: 0 1 2 3 .(period) | | * Color Space Only: 0 1 2 3 .(period) |
| * Base or Color Space: A C T G N a c t g n 0 1 2 3 .(period) | | * Base or Color Space: A C T G N a c t g n 0 1 2 3 .(period) |
− | | ERROR on Line <current line #>: | + | | 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. | | | 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. | | * 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 #>: | + | | 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). | | | Each Line of a Raw Sequence should have at least 1 character (not be blank). |
− | | ERROR on Line <current line #>: | + | | ERROR on Line <current line #>: Looking for continuation of Raw Sequence or '+' instead found a blank line, assuming it was part of Raw Sequence. |
| |} | | |} |
| | | |
Line 49: |
Line 49: |
| |- | | |- |
| | Must exist for every sequence. | | | Must exist for every sequence. |
− | | ERROR on Line <current line #>: | + | | 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. | | | If the optional sequence identifier is specified, it must equal the one on the Sequence Identifier Line. |
− | | ERROR on Line <current line #>: | + | | ERROR on Line <current line #>: Sequence Identifier on '+' line does not equal the one on the '@' line. |
| |} | | |} |
| | | |
Line 62: |
Line 62: |
| |- | | |- |
| | A quality string should be present for every base sequence. | | | A quality string should be present for every base sequence. |
− | | ERROR on Line <current line #>: | + | | 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. | | | Paired quality and base sequences should be of the same length. |
− | | ERROR on Line <current line #>: | + | | 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. | | | Valid quality values should all have ASCII codes > 32. |
− | | ERROR on Line <current line #>: | + | | ERROR on Line <current line #>: Invalid character ('<invalid char>') in quality string. |
| |} | | |} |
| | | |