Regular Expressions to describe attributes in read descriptors

Regular expressions allow for a flexible description of attribute retrieval from generic read descriptors. A summary of the regular expression system adopted in the Flux Capacitor can be found there.

Example 1

chr1    10033   10109   PAN:2:27:1091:1987/2

the example shows a standard Illumina/Solexa identifier for paired sequencing, where /1 indicates the first mate of a pair and /2 the second mate. A corresponding regular expression would target the suffix by


Example 2

chr1    10033   10109   PAN:2:27:1091:1987/2_strand1

where /2 indicates the 2nd mate, and '_strand1' additionally indicates read orientation in sense to the transcription directionality could be described by the regular expression


Note: exactly two symbols are expected for identifying paired mates as well as sense/anti-sense orientation. In the case the information is optional, add

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