BAMALIGNFRAC(1)

✨ NAME ✨

bamalignfrac — bestie, it computes the fraction of aligned bases in an alignment file 💅

This one's from the General Commands Manual, and yes she is that girl.

🌸 SYNOPSIS 🌸

bamalignfrac [options] <input.bam>

🦋 DESCRIPTION 🦋

okay so bamalignfrac reads a SAM/BAM/CRAM file, does a whole lil math moment, and prints a set of statistical values on the standard output channel. no cap. here's what she gives you:

• the number of names passing a given regex filter 👑
• the number of primary alignments
• the number of total alignments
• the total number of bases
• the total number of aligned bases
• the fraction of aligned bases 🎀
• the total number of clipped/unaligned bases
• the number of unmapped reads 💀

all of these get printed on the standard output channel at the end of the program run, in the last line printed by the program. before that, the program prints a set of line description lines. so like, the receipts come first, then the ✨numbers✨.

🫶 heads up bestie: the input file needs to be provided in query name sorted order. you can get that via e.g.

$ bamsort SO=queryname

right before being passed to bamalignfrac. do not skip this step, i'm literally begging 🙈

The following key=value pairs can be given:

• verbose=<0|1> — print preliminary values for file prefixes while processing the input file 👀
• name=<> — only consider reads matching the given regular expression. by default all reads are considered, no filtering, we love an inclusive queen 💖

💜 AUTHOR 💜

Written by German Tischler-Höhle. icon behavior fr fr.

😭 REPORTING BUGS 😭

Report bugs to <germant@miltenyibiotec.de>. she wants to hear from you, tell her everything.

👑 COPYRIGHT 👑

Copyright © 2009-2019 German Tischler, © 2011-2013 Genome Research Limited. License GPLv3+: GNU GPL version 3 <http://gnu.org/licenses/gpl.html>

This is free software: you are free to change and redistribute it.

🚨 There is NO WARRANTY, to the extent permitted by law. (so true, so real, protect yourself)

and that's the whole page bestie, mwah 💋 — this was the BIOBAMBAM era, July 2019, filed under BAMALIGNFRAC(1). slay, periodt. 💅✨🎀