Crate fasten_pe

Determine paired-end-ness in an interleaved file. Exit code of 0 indicates PE. Exit code > 0 indicates single end.

Examples

Test the file and then print a message with the exit code

cat file.fastq | fasten_pe; echo "Reads were paired-end? $?";

Test the file and if it is paired end (exit code 0), then print a message

cat file.fastq | fasten_pe || echo "Reads were paired end.";

Usage

Usage: fasten_pe [-h] [-n INT] [-p] [-v] [--print-reads]
 
Options:
    -h, --help          Print this help menu.
    -n, --numcpus INT   Number of CPUs (default: 1)
    -p, --paired-end    The input reads are interleaved paired-end
    -v, --verbose       Print more status messages
        --print-reads   Print each read. Useful for Unix pipes.

Functions

is_paired_end_miseq

Detect whether the vector of IDs represent paired-endedness with finding out whether they fit the pattern shown in Illumina documentation at http://support.illumina.com/content/dam/illumina-support/help/BaseSpaceHelp_v2/Content/Vault/Informatics/Sequencing_Analysis/BS/swSEQ_mBS_FASTQFiles.htm

is_paired_end_slash12

Detect whether the vector of IDs represent paired-endedness with finding out whether they end with /1 and /2.

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