BAMAUXMERGE(1)

💖 BAMAUXMERGE 💖

okay bestie, so bamauxmerge is literally the girlboss of the biobambam fam — she takes your unmapped reads file and your mapped reads file and merges them together into one gorgeous little alignment file ✨ no cap.

---

✨ NAME ✨

bamauxmerge — merge information in unmapped and mapped alignment files 🧬💅

---

🌸 SYNOPSIS 🌸

bamauxmerge [options] in_unmapped in_mapped

---

🦋 DESCRIPTION 🦋

So like. bamauxmerge reads and merges two SAM/BAM/CRAM files, and those two files are expected to have these specific properties, okay? vibe check:

• the first file contains only unmapped reads and its header contains no SQ lines
• the second file was produced by an aligner based on the content of the first file.
• the order of the reads is the same in the first an second file into a single alignment file.

The way the headers of the two files get merged, it's giving:

• the SQ lines contained in the header of the second file are appended to the header of the first file to obtain the header of the output file
• all other header information from the second file is discarded 🙈 (bye girl, we don't know her)

And the output records? Constructed like this, periodt:

1. Take a record from the second file
2. Copy all aux fields from the corresponding record in the first file which are not already present.

Now here's the part where you gotta pay attention bestie — the following key=value pairs can be given:

• level=<-1|0|1|9|11> — set compression level of the output BAM file. Valid values are:
  • -1: zlib/gzip default compression level
  • 0: uncompressed
  • 1: zlib/gzip level 1 (fast) compression
  • 9: zlib/gzip level 9 (best) compression

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 an additional valid value is:

• 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 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.
• 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:
  • bam: BAM (see http://samtools.sourceforge.net/SAM1.pdf)
  • sam: SAM (see http://samtools.sourceforge.net/SAM1.pdf)
  • cram: CRAM (see http://www.ebi.ac.uk/ena/about/cram_toolkit)
• 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:
  • bam: BAM (see http://samtools.sourceforge.net/SAM1.pdf)
  • sam: SAM (see http://samtools.sourceforge.net/SAM1.pdf)
  • cram: CRAM (see http://www.ebi.ac.uk/ena/about/cram_toolkit). This format is not advisable for data sorted by query name. ⚠️
• inputthreads=<[1]> — input helper threads, only valid for inputformat=bam.
• outputthreads=<[1]> — output helper threads, only valid for outputformat=bam.

---

👑 AUTHOR 👑

Written by German Tischler. 💜

---

🎀 REPORTING BUGS 🎀

Report bugs to <germant@miltenyibiotec.de> — bestie will literally fix it, fr fr. 🫶

---

🌈 COPYRIGHT 🌈

Copyright © 2009-2013 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. 💀

---

okay that's the whole thing, no gatekeeping here 💅

and that's a wrap, my love — this page came to you courtesy of BIOBAMBAM, dated July 2013, and yeah, she's still iconic. mwah 🍓✨