BAMFILLQUERY(1)

📦 version 2.0.185, in debian bookworm, debian trixie, ubuntu jammy, ubuntu noble, ubuntu questing, ubuntu resolute, ubuntu stonking

💖 BAMFILLQUERY 💖

okay bestie, welcome to bamfillquery from the BIOBAMBAM collection — General Commands Manual energy, group-chat delivery. sit down, hydrate, let's go 🫶

✨ NAME ✨

bamfillquery — fill query sequences into BAM files 🧬✨

🌸 SYNOPSIS 🌸

bamfillquery [options] <in.bam queries.fasta >out.bam

🦋 DESCRIPTION 🦋

so basically bamfillquery reads a SAM/BAM/CRAM file and a FastA file, copies the sequences it finds in that FastA file into the query sequence field of the SAM/BAM/CRAM file, and writes the whole resulting glow-up out to a SAM/BAM/CRAM file. it's giving "put the sequence back where it belongs" 💅

⚠️ heads up bestie: both the alignment input file and the FastA file need to be sorted by query name. no cap. if they're not, go see bamsort or bamsormadup to get the SAM/BAM/CRAM file into that order first. 🙈

The following key=value pairs can be given:

🎀 level=<-1|0|1|9|11>

set the compression level of the output BAM file. the valid values are, and I quote:

  • -1 — zlib/gzip default compression level
  • 0 — uncompressed
  • 1 — zlib/gzip level 1 (fast) compression
  • 9 — zlib/gzip level 9 (best) compression

and if libmaus has been compiled with support for igzip (see https://software.intel.com/en-us/articles/igzip-a-high-performance-deflate-compressor-with-optimizations-for-genomic-data) then there's one more valid value for you:

  • 11 — igzip compression 🔥

🎀 verbose=<1>

valid values are:

  • 1 — print progress report on standard error
  • 0 — do not print progress report

🎀 tmpfile=<filename>

prefix for temporary files. by default the temporary files are created in the current directory. 🗂️

🎀 md5=<0|1>

md5 checksum creation for the output file. valid values are:

  • 0 — do not compute checksum. this is the default.
  • 1 — compute checksum. if the md5filename key is set, then the checksum is written to the given file. if md5filename is unset, then no checksum will be computed. (yes, really — set the key, bestie 💀)

🎀 md5filename

file name for md5 checksum if md5=1.

🎀 index=<0|1>

compute BAM index for output file. valid values are:

  • 0 — do not compute BAM index. this is the default.
  • 1 — compute BAM index. if the indexfilename key is set, then the BAM index is written to the given file. if indexfilename is unset, then no BAM index will be computed.

🎀 indexfilename

file name for BAM index if index=1.

🎀 inputformat=<bam>

input file format. all versions of bamsort come with support for the BAM input format. if the program in addition is linked to the io_lib package, then the following options are valid:

🎀 outputformat=<bam>

output file format. all versions of bamsort come with support for the BAM output format. if the program in addition is linked to the io_lib package, then the following options are valid:

🎀 I=<[stdin]>

input filename, standard input if unset. 🌊

🎀 O=<[stdout]>

output filename, standard output if unset. 🌊

🎀 inputthreads=<[1]>

input helper threads, only valid for inputformat=bam. ⚡

🎀 outputthreads=<[1]>

output helper threads, only valid for outputformat=bam. ⚡

🎀 reference=<[]>

reference FastA file for inputformat=cram and outputformat=cram. an index file (.fai) is required. 📎

👑 AUTHOR 👑

Written by German Tischler. (an icon, fr fr)

🐛 REPORTING BUGS 🐛

Report bugs to <germant@miltenyibiotec.de>

Copyright © 2009-2016 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.

and that's the whole page, bestie 🫶 this was the BIOBAMBAM release, dated August 2017 — BAMFILLQUERY(1), out. slay, stay sorted by query name, and drink some water 💖✨🎀🦋🌸

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