Shore merge

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shore merge merges and filters alignment files.

Command line options

Usage: shore merge [OPTIONS] [ALIGNMENT_PATHS]

-m, --infiles=<arg[,...]> Alignment files or shore directories (run, lane, read or sample; comma-separated; defaults to <outdir>)
-I, --idordered Input alignments are sorted by read ID and not by coordinate
Main output options
-o, --outdir=<arg> (Default: AlignmentFolder) Set output directory (will be created if necessary)
-A, --no-alignments Deactivate processing of alignment files (only merge insert size distributions or left over files)
-l, --leftovers Activate merging of leftover reads
-p, --rplot Graphical output of statistics using R
Ancillary output options
-s, --subsamples=<arg[,...]> Generate random subsamples of <arg> reads
--diff Write all reads that only occur in a single alignment file
--phasesplit=<arg> Split reads by <arg>-mer phasing
--combine Combine alignments (discard duplicate entries and alignments that are not the best hit)
-q, --stats-only Statistics only, do no write the merged data
-t, --no-stats Disable alignment statistic
-Z, --nocompress Do no compress output files
-S, --stdout Don't create an output directory, write alignments to standard output (implies -t, -Z)
Alignment filter
-H, --hits-range=<arg,arg> Set the allowed range of repetitiveness ('1,1' = nonrep reads)
-M, --mm-range=<arg,arg> Set the allowed range of mismatches
-R, --region=<arg> Only use reads that overlap with the range [chr1:pos1..[chr2:]pos2]
--assume-length=<arg> (Default: 400) Assume maximal alignment length <arg>, enables fast range queries
-X, --p3fix=<arg> Set the 3' end to a fixed distance from the 5' end
-N, --read-lengths=<arg[,...]> Use only reads of the given length(s)
-T, --strand=<arg> Use only reads from the given strand
-B, --duplicates=<arg> Report at maximum <arg> reads with the 5' end at the same position on the same strand
--wpoiss=<arg> Window size for adaptive duplicate read filtering
--sam-ref=<arg> Reference sequence for SAM file parsing
--peflags=<arg[,...]> Use only reads with the given PE flag(s)
Leftover filter
--badqual=<arg> (Default: 10) Quality threshold
--maxbadbases=<arg> (Default: 8) Max. number low quality bases