FASTQTOBAM(1)

💖 NAME 💖

hey bestie, welcome to FASTQTOBAM(1) — it lives in the General Commands Manual section and its whole personality is:

fastqtobam — convert FastQ to unmapped BAM ✨

that's it, that's the job, and it does it flawlessly.

🌈 SYNOPSIS 🌈

fastqtobam [options]

🎀 DESCRIPTION 🎀

okay so here's the vibe 🫶 fastqtobam reads one or two FastQ files and converts them into a BAM file where every single read is marked as unmapped. no cap.

Here's how the input situation works, and yes you need to know this:

• No input file name given? Then a single FastQ file is read from standard input.
• One file name given? Then a single FastQ file is read from that given file. In both of those cases, the read names in the file get parsed to figure out whether the reads inside are paired or not — unless the name scheme is set to pairedfiles.
• Two file names given? Then the program assumes it's looking at two FastQ files that are synchronous, i.e. the first read in the first file is the mate of the first read in the second file, and so on down the line.

Input file names can be handed over either via the I key or after the key=value pairs on the command line. The program accepts the read name formats described below under the key name namescheme. 💅

The following key=value pairs can be given:

• verbose=<[0|1]> — print a progress report. By default, progress is not reported. sad but true.
• I=<filename> — input file name (data is read from standard input if this option isn't given). This key can be given twice. 👯
• level=<-1|0|1|9|11> — set the 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

And if libmaus has been compiled with support for igzip (peep https://software.intel.com/en-us/articles/igzip-a-high-performance-deflate-compressor-with-optimizations-for-genomic-data), then there's an additional valid value:

• 11: igzip compression

• md5=<0|1> — md5 checksum creation for the output file. Valid values are:
  • 0: do not compute a checksum. This is the default.
  • 1: compute a checksum. If the md5filename key is set, then the checksum gets written to the given file. If md5filename is unset, then no checksum will be computed.
• md5filename — file name for the md5 checksum if md5=1.
• gz=<[0|1]> — input is gzip compressed FastQ. By default the input is assumed to be uncompressed FastQ.
• threads=<1> — additional BAM encoding helper threads. 🧵
• PGID=<> — read group identifier for reads. By default no read group identifier is set. The fields CN, DS, DT, FO, KS, LB, PG, PI, PL, PU and SM of the corresponding @RG header line can be set by using the keys RGCN, RGDS, etc. respectively. 👑
• qualityoffset=<33> — FastQ quality offset. This value is subtracted from the ASCII character representation to get the quality score value.
• qualitymax=<41> — maximum valid quality value, 41 by default. Higher values may indicate a wrong setting of the qualityoffset parameter. BAM allows quality values up to the value of 94.
• qualityhist=<0> — compute a quality histogram and print it on the standard error channel after processing has finished successfully. Lines for the quality histogram are prefixed with [H] and contain tab separated values. The histogram enumerates quality scores from high to low values. The histogram has four columns (after the [H] marker). The first is the ASCII representation of the quality with offset 33, i.e. the symbol ! denotes quality 0. The second column gives the absolute frequency of the value. The third column stores the relative frequency of the value, i.e. the fraction of all values assigned to this value. The fourth column gives a cumulative relative frequency value over all quality for the current line and those for higher quality values. 📊
• checkquality=<1> — check whether quality values are in range and terminate if an invalid value is encountered.
• namescheme=<generic> — read name scheme. This determines how read names are parsed. There are four possible options:
  • generic: the first sequence of non whitespace characters is extracted from the @ line of the FastQ record and the rest of the @ line is discarded. If the retained name ends in /1 or /2, then the read is part of a read pair, otherwise it is the single read for the template. For a pair, the part of the name before the /1 or /2 is considered the template name. For a single, the whole name is considered the name of the template.
  • c18s: The name is expected to consist of two sequences of non white-space characters where the first contains seven colon separated fields and the second four colon separated fields. The first of the two is considered to be the name of the template. It is assumed that this read is the only read for the template.
  • c18pe: As for c18s, the name is expected to consist of two sequences of non white-space characters where the first contains seven colon separated fields and the second four colon separated fields. The first of the two is considered to be the name of the template. The read is assumed to be part of a read pair. The first field in the second non-whitespace sequence of the @ line designates whether it is the first or second of the pair, depending on whether the field stores the number 1 or 2 respectively.
  • pairedfiles: The input framgents are assumed to be paired. If there is a single input file then the pairs are expected consecutive in the file. If there are two input files then the read names in the two are expected to be synchronous. All characters in read names beginning from the first white space character are discarded. If the two (so reduced) read names in question end on /1 and /2 respectively, then those suffixes will be clipped off also. The remaining read names are checked for equality. If they are not equal, then the program will reject the input and terminate. 💀
• chksumfn=<> — File name used for storing bamseqchksum like information about the output file. By default no such file is produced.
• hash=<crc32prod> — Hash used for producing bamseqchksum type information. The information produced is only stored if the chksumfn option is set.

✨ AUTHOR ✨

Written by German Tischler. 💜

🐛 REPORTING BUGS 🐛

Report bugs to <germant@miltenyibiotec.de> — they want to hear from you fr fr.

👑 COPYRIGHT 👑

Copyright © 2009-2014 German Tischler, © 2011-2014 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, we ate 🍓 this was BIOBAMBAM, dated July 2013 — iconic behavior, no notes, mwah 💅💖