fastqrab documentation

Mon, 01 Jan 0001 00:00:00 +0000

ValidateAllReadsSameLength #

[[step]]
 action = "ValidateAllReadsSameLength"
 source = "read1" # Any segment, All, tag:<name> or 'name:segment>'

Validates that all reads have the same sequence/tag/name length.

Useful when you want to verify read length consistency in your pipeline.

(For names, the names without comments - that is up to the first input.options.read_comment_character are used).

Mon, 01 Jan 0001 00:00:00 +0000

ValidateName #

Verify that all segments have the same read name (or a shared prefix).

[[step]]
 action = "ValidateName"
 # Optional separator character; the comparison stops at the first match
 readname_end_char = "_" # Optional. Do not set for exact matching. Otherwise, a byte character
 sample_stride = 1000 # Check every nth fragment, default 1000. Must be > 0. Starts with first read

When no separator character (readname_end_char) is provided the entire name must match exactly across all segments.

Mon, 01 Jan 0001 00:00:00 +0000

ValidateQuality #

Validate that all scores are between 33..=41

[[step]]
 action = "ValidateQuality"
 segment = "read1" # Any of your input segments, or 'All'
 encoding = 'Illumina1.8' # 'Illumina1.8|Illumina1.3|Sanger|Solexa'
 # Illumina1.8 is an alias for Sanger.

The encoding defines the accepted range of values.

If you want to convert quality codes, use ConvertQuality.

See https://pmc.ncbi.nlm.nih.gov/articles/PMC2847217/ , table 1

Mon, 01 Jan 0001 00:00:00 +0000

ValidateReadNamesPrintable #

Validate that every read name conforms to the SAM/BAM specification.

The SAM specification requires that query names (QNAME) match [!-?A-~]{1,254}: printable ASCII characters excluding @ and space, with a maximum length of 254.

[[step]]
 action = "ValidateReadNamesPrintable"

No additional parameters are needed — the allowed character set is fixed by the SAM spec.

When to use #

Add this step when your pipeline writes non-BAM output that will become BAM eventually and you suspect read names may contain invalid characters.

Mon, 01 Jan 0001 00:00:00 +0000

ValidateReadPairing #

Confirms for every sample_strideth read ‘pair’ that the names are identical but for one letter.

[[step]]
 action = "ValidateReadPairing"
 sample_stride = 1000 # Check every nth fragment, default 1000. Must be > 0. Starts with first read

Ensures

read names between segments have the same length
read names between segments have a hamming distance of at most one.

Note that this validation requires at least two input segments.

(See also: ValidateName, which validates after truncating on a character occurance).

Mon, 01 Jan 0001 00:00:00 +0000

ValidateSeq #

Validate that only allowed characters are in the sequence.

[[step]]
 action = "ValidateSeq"
 allowed = "AGTC" # String. Example 'ACGTN', the allowed characters
 segment = "read1" # Any of your input segments, or 'All'