Difference between revisions of "FastQValidator"

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(Valid FastQ File Requirements)
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A valid fastQ file meets the validation criteria specified in [[FastQFile#Validation Criteria Used For Reading a Sequence|FastQ File Validation]].
 
A valid fastQ file meets the validation criteria specified in [[FastQFile#Validation Criteria Used For Reading a Sequence|FastQ File Validation]].
 +
 +
 +
== How to Use the fastQValidator Executable ==
 +
'''Required Parameters:'''
 +
        --file  :  FastQ filename with path to be prorcessed.
 +
 +
'''Optional Parameters:'''
 +
        --minReadLen        : Minimum allowed read length (Defaults to 10).
 +
        --maxReportedErrors : Maximum number of errors to display before suppressing them (Defaults to 20).
 +
        --ignoreAllErrors  : Ignore all errors (same as --maxReportedErrors 0), overwrites the maxReportedErrors option.
 +
 +
'''Optional Space Options for Raw Sequence (Last one specified is used):'''
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        --autoDetect : Determine baseSpace/colorSpace from the Raw Sequence in the file (Default).
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        --baseSpace  : ACTGN only
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        --colorSpace : 0123. only
 +
 +
'''Usage:'''
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        ./fastQValidator --file <fileName> [--minReadLen <minReadLen>] [--maxReportedErrors <maxReprotedErrors>|--ignoreAllErrors] [--baseSpace|--colorSpace|--autoDetect]
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 +
'''Examples:'''
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        ../fastQValidator --file testFile.txt
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        ../fastQValidator --file testFile.txt --minReadLen 10 --baseSpace --maxReportedErrors 100
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        ./fastQValidator --file test/testFile.txt --minReadLen 10 --colorSpace --ignoreAllErrors
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 +
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== FastQ Validator Output ==
 +
When running the fastQValidator Executable, the output starts with a summary of the parameters:
 +
 +
The following parameters are in effect:
 +
 +
Input Parameters
 +
--file [testFile.txt], --minReadLen [10]
 +
  Space Type : --baseSpace [ON], --colorSpace, --autoDetect
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      Errors : --ignoreAllErrors, --maxReportedErrors [100]
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 +
The Validator Executable outputs error messages for invalid sequences based on [[FastQFile#Validation Criteria Used For Reading a Sequence|Validation Criteria]].
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For Example:
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ERROR on Line 25: The sequence identifier line was too short.
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ERROR on Line 29: First line of a sequence does not begin wtih @
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ERROR on Line 33: No Sequence Identifier specified before the comment.
 +
 +
Base Composition Percentages by Index:
 +
 +
Base Composition Statistics:
 +
Read Index %A %C %G %T %N Total Reads At Index
 +
        0  100.00    0.00    0.00    0.00    0.00 20
 +
        1    5.00  95.00    0.00    0.00    0.00 20
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        2    5.00    0.00    5.00  90.00    0.00 20
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 +
 +
Summary of the number of lines, sequences, and errors:
 +
Finished processing testFile.txt with 92 lines containing 20 sequences.
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There were a total of 17 errors.
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== Additional Features ==
 
== Additional Features ==
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* It may be useful to report 2 types of information to the user: ERROR (critical failure) and WARNING (tolerable errors).
 
* It may be useful to report 2 types of information to the user: ERROR (critical failure) and WARNING (tolerable errors).
 
 
 
== How to Use the fastQValidator Executable ==
 
'''Required Parameters:'''
 
        -f  :  FastQ filename with path to be prorcessed.
 
 
'''Optional Parameters:'''
 
        -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: "A"/"C"/"G"/"T"/"N"  - Bases only;
 
                                  "0"/"1"/"2"/"3"/"."  - Color space only;
 
                                  ""                  - Base Decision on the first Raw Sequence Character (Default)
 
                                  All other characters - Bases & Color space
 
 
'''Testing only Parameters:'''
 
        -t  :  If "ReadOnly" is specified, the fastq will be read but not processed.  This may be used for determining read time.
 
'''Usage:'''
 
        ./fastQValidator -f <fileName> -l <minReadLen> -e <maxReprotedErrors> -b <rawSeqType>
 
 
'''Examples:'''
 
        ../fastQValidator -f testFile.txt
 
        ../fastQValidator -f testFile.txt -l 10 -b A -e 100
 
        ./fastQValidator -f test/testFile.txt -l 10 -b Z -e 100
 
        time ./fastQValidator -f test/testFile.txt -t ReadOnly
 
 
 
== FastQ Validator Output ==
 
When running the fastQValidator Executable, the output starts with a summary of the parameters:
 
The following parameters are in effect:
 
              FastQ File Name :    testFile.txt (-fname)
 
              Min Read Length :              10 (-l9999)
 
          Max Reported Errors :            100 (-e9999)
 
                      BaseType :              A (-bname)
 
                      TestMode :                (-tname)
 
 
Both the Executable and the Library outputs the following:
 
*Error messages for the first Configurable number of errors.:
 
ERROR on Line 25: The sequence identifier line was too short.
 
ERROR on Line 29: First line of a sequence does not begin wtih @
 
ERROR on Line 33: No Sequence Identifier specified before the comment.
 
*Base Composition Percentages by Index:
 
 
Base Composition Statistics:
 
Read Index %A %C %G %T %N Total Reads At Index
 
        0  100.00    0.00    0.00    0.00    0.00 20
 
        1    5.00  95.00    0.00    0.00    0.00 20
 
        2    5.00    0.00    5.00  90.00    0.00 20
 
*Summary of the number of lines, sequences, and errors:
 
Finished processing testFile.txt with 92 lines containing 20 sequences.
 
There were a total of 17 errors.
 

Revision as of 14:16, 22 February 2010

Status

The initial version of a FastQ Validator is complete.


Valid FastQ File Requirements

A valid fastQ file meets the validation criteria specified in FastQ File Validation.


How to Use the fastQValidator Executable

Required Parameters:

       --file  :  FastQ filename with path to be prorcessed.

Optional Parameters:

       --minReadLen        : Minimum allowed read length (Defaults to 10).
       --maxReportedErrors : Maximum number of errors to display before suppressing them (Defaults to 20).
       --ignoreAllErrors   : Ignore all errors (same as --maxReportedErrors 0), overwrites the maxReportedErrors option.

Optional Space Options for Raw Sequence (Last one specified is used):

       --autoDetect : Determine baseSpace/colorSpace from the Raw Sequence in the file (Default).
       --baseSpace  : ACTGN only
       --colorSpace : 0123. only

Usage:

       ./fastQValidator --file <fileName> [--minReadLen <minReadLen>] [--maxReportedErrors <maxReprotedErrors>|--ignoreAllErrors] [--baseSpace|--colorSpace|--autoDetect]

Examples:

       ../fastQValidator --file testFile.txt
       ../fastQValidator --file testFile.txt --minReadLen 10 --baseSpace --maxReportedErrors 100
       ./fastQValidator --file test/testFile.txt --minReadLen 10 --colorSpace --ignoreAllErrors


FastQ Validator Output

When running the fastQValidator Executable, the output starts with a summary of the parameters:

The following parameters are in effect:
Input Parameters
--file [testFile.txt], --minReadLen [10]
  Space Type : --baseSpace [ON], --colorSpace, --autoDetect
      Errors : --ignoreAllErrors, --maxReportedErrors [100]

The Validator Executable outputs error messages for invalid sequences based on Validation Criteria. For Example:

ERROR on Line 25: The sequence identifier line was too short.
ERROR on Line 29: First line of a sequence does not begin wtih @
ERROR on Line 33: No Sequence Identifier specified before the comment.

Base Composition Percentages by Index:

Base Composition Statistics:
Read Index	%A	%C	%G	%T	%N	Total Reads At Index
        0   100.00    0.00    0.00    0.00    0.00	20
        1     5.00   95.00    0.00    0.00    0.00	20
        2     5.00    0.00    5.00   90.00    0.00	20


Summary of the number of lines, sequences, and errors:

Finished processing testFile.txt with 92 lines containing 20 sequences.
There were a total of 17 errors.


Additional Features

  • Base composition reported and tracked by position.
  • Supports base space and color space files.
  • Consumes gzipped and uncompressed text files transparently.
  • Prints error messages for errors up to the configurable maximum number of reportable errors.
  • Prints a summary of the total number of errors.
  • Prints the total number of lines processed as well as the total number of sequences processed.


Additional Wishlist - Not Implemented

There are a series of optional capabilities a FastQ Validator could implement. Among those:

  • 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).


Discussion

  • For color space, there is no specification for:
  1. The length of read and quality string may be the same or differs by 1 (depending on whether the primer base has a corresponding quality value).
  2. Missing values are usually presented by "." or sometimes left as a blank " ".
  3. Tag names for paired end reads may be the same (e.g. MAQ actually enforces that), and may be in the same file (e.g. BFAST require paired reads in the same file)
  • It may be useful to report 2 types of information to the user: ERROR (critical failure) and WARNING (tolerable errors).