mbf-fastq-processor documentation

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

SpotCheckReadPairing #

Confirms for every sample_strideth read ‘pair’ that the names share the same prefix (part before ‘readname_end_char’).

[[step]]
 action = "SpotCheckReadPairing"
 sample_stride = 1000 # Every nth fragment, default 1000. Must be > 0. 
 readname_end_char = '/' # u8/byte-char, Defaults to no character, meaning the entire name is compared.

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

Otherwise the read names are truncated after the first readname_end_char, and the prefixes must match exactly. For example, use readname_end_char = “_” for typical Illumina _1/_2 suffixes.

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/read length.

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

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

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

Otherwise the read names are truncated after the first readname_end_char, and the prefixes must match exactly. For example, use readname_end_char = "_" for typical Illumina _1/_2 suffixes.

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

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'