Module seq_io 

Structs

InterleavedFastqReader

Read that reads an interleaved paired end FASTQ file.

InterleavedRecordSet

Thin wrapper around a RecordSet that contains an even number of records, with interleaved read spairs.

PairedFastqReader

Reader for paired ends that are spread across two FASTQ files. The number of records read from each file is synchronized, but the number is not known until after reading the first time, when we determine how many reads can fit into the fixed size buffer. While the buffer may grow later for each RecordSet later (if later reads are longer), this is a good approximation given the buffer size.

PairedRecordSetIterator

Iterator over paired end reads from two FASTQ files.

RecordSetTuple

Stores two record sets with the same number of records for paired end reads. Each record set is used to read from the corresponding reader, one per end of a pair.

Functions

parallel_interleaved_fastq

Function reading records in a different thread. processing them in another worker thread and finally returning the results to the main thread.

parallel_interleaved_fastq_init

More customisable function doing per-record processing with closures for initialization and moer options.

parallel_paired_fastq

Function reading records in a different thread. processing them in another worker thread and finally returning the results to the main thread.

parallel_paired_fastq_init

More customisable function doing per-record processing with closures for initialization and moer options.