Revision as of 17:44, 3 February 2010 by Mktrost
Sequence Identifier Line
- Every entry in the file should have a unique identifier.
Raw Sequence Line
- A base sequence should have non-zero length.
- Validates the base sequences against the characters allowed via configuration.
- Base Only: A C T G N a c t g n
- 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)
- Reads should be of a minimum length; many mappers will get into trouble with very short reads.
Quality String Line
- A quality string should be present for every base sequence.
- Paired quality and base sequences should be of the same length.
- Valid quality values should all have ASCII codes > 32.
- Base composition are reported and tracked by position.
- Consumes gzipped and uncompressed text files transparently (see libcsg/InputFile.h).
Additional Wishlist - Not Implemented
- To reduce memory usage, implement a two-pass algorithm that stores only a key for each sequence name (rather than complete sequence names) in memory (suggest a pair of options -1 -> one pass, high memory use, -2 -> two pass lower memory use, default is -1).
How to Use the fastQValidator Executable
-f : FastQ filename with path to be prorcessed.
-l : Minimum allowed read length (Defaults to 10). -e : Maximum number of errors to display before suppressing them(Defaults to 20). -b : Raw sequence type: B - ACTGN only (Default) C - 0123. only BC - ACTGN or 0123.
Testing only Parameters:
-t : If "ReadOnly" is specified, the fastq will be read but not processed. This may be used for determining read time.
./fastQValidator -f <fileName> -l <minReadLen> -e <maxReprotedErrors> -b <rawSeqType>
../fastQValidator -f testFile.txt ../fastQValidator -f testFile.txt -l 10 -b BC -e 100 ./fastQValidator -f test/testFile.txt -l 10 -b BC -e 100 time ./fastQValidator -f test/testFile.txt -t ReadOnly
FastQ Validator Output