RABEMA_BUILD_GOLD_STANDARD(1)

📦
version 2.5.2 · 2 versions
, in ubuntu stonking

🦋 rabema_build_gold_standard — RABEMA Gold Standard Builder 🦋

hiii bestie welcome to section 1 of the manual 💖 this is rabema_build_gold_standard, she builds gold standards, she's the moment, she knows exactly what she's doing and honestly? obsessed with her. let's get into it ✨

✨ NAME ✨

rabema_build_gold_standard — the RABEMA Gold Standard Builder. that's her name and her entire personality, and she ate. 💅

🌈 SYNOPSIS 🌈

rabema_build_gold_standard [OPTIONS] --out-gsi OUT.gsi --reference REF.fa --in-bam PERFECT.{sam,bam}

so like. [OPTIONS] is the fun flexible part, but then she needs three things from you: where the gold standard goes (--out-gsi), your reference (--reference), and your perfect map (--in-bam). not optional bestie, she means it 🫶

🧚 DESCRIPTION 🧚

okay so this program lets you build a RABEMA gold standard. the input is a reference FASTA file and a perfect SAM/BAM map — perfect like, e.g. one created using RazerS 3 in full-sensitivity mode. no cap, that's the vibe. 💖

⚠️ bestie. the input SAM/BAM file must be sorted by coordinate. this is not a suggestion, this is the law, and she will know if you skipped it.

also she's gonna create a FASTA index file REF.fa.fai so she can do fast random access into the reference. cute of her, honestly. 🎀

💅 OPTIONS 💅

  • -h, --help — pop the help message. your emotional support flag. 🌸
  • --version — shows you the version info. she's telling you exactly who she is. 👑
  • -v, --verbose — turns on verbose output. she talks more. you get more. 💬
  • -vv, --very-verbose — even more verbose output. she is telling you EVERYTHING and honestly good for her. 🔥

📥 Input / Output: 📤

  • -o, --out-gsi OUTPUT_FILE — the path where the resulting GSI file gets written. valid filetype is .gsi[.*], and that * can be: gz for transparent (de)compression. ✨
  • -r, --reference INPUT_FILE — the path to load the reference FASTA from. valid filetypes are: .sam[.*], .raw[.*], .gbk[.*], .frn[.*], .fq[.*], .fna[.*], .ffn[.*], .fastq[.*], .fasta[.*], .fas[.*], .faa[.*], .fa[.*], .embl[.*], and .bam, where * is any of the following extensions: gz, bz2, and bgzf for transparent (de)compression. like. she really said "bring me a format, any format" 😭
  • -b, --in-bam INPUT_FILE — the path to load the "perfect" SAM/BAM file from (quotes are hers, she's being cute about it). valid filetypes are: .sam[.*] and .bam, where * is any of the following extensions: gz, bz2, and bgzf for transparent (de)compression. 🦋

🏆 Gold Standard Parameters: 🏆

  • --oracle-mode — enables oracle mode. this one's for simulated data, when the input SAM/BAM file gives you exactly one position that counts as the true sample position. one. single. position. main character energy, truly. 🔮
  • --match-N — when you set this, N matches all characters without penalty. she said no consequences for N, iykyk. 💫
  • --distance-metric STRING — sets the distance metric. valid values: hamming, edit. Default: edit. One of hamming and edit. Default: edit. yeah she said it twice, she's thorough like that 💅
  • -e, --max-error INTEGER — the maximal error rate to build the gold standard for, in percent. this parameter is an integer and it's relative to the read length. in the case of oracle mode, the error rate for the read at the sampling position is used and RATE is used as a cutoff threshold. Default: 0. 📏

🌟 RETURN VALUES 🌟

a return value of 0 means success 🎉 and any other value means an error 😭. that's it, that's the whole system, she keeps it simple.

🌸 EXAMPLES 🌸

1.

rabema_build_gold_standard -e 4 -o OUT.gsi -s IN.sam -r REF.fa

build gold standard from a SAM file IN.sam with all mapping locations and a FASTA reference REF.fa to GSI file OUT.gsi with a maximal error rate of 4. 🔥

2.

rabema_build_gold_standard --distance-metric edit -e 4 -o OUT.gsi -b
IN.bam -r REF.fa

same as above, but using Hamming instead of edit distance and BAM as the input. (yes bestie, she passed --distance-metric edit and then said "instead of edit distance" — she contains multitudes, we don't question the queen 😭👑)

3.

rabema_build_gold_standard --oracle-mode -o OUT.gsi -s IN.sam -r REF.fa

build gold standard from a SAM file IN.sam with the original sample position, e.g. as exported by read simulator Mason. 🔮✨

🧠 MEMORY REQUIREMENTS 🧠

from version 1.1, great care has been taken to keep the memory requirements as low as possible. 💖 the memory required is two times the size of the largest chromosome plus some constant memory for each match.

for example, the memory usage for 100bp human genome reads at 5% error rate was 1.7GB. of this, roughly 400GB came from the chromosome and 1.3GB from the matches. (she said what she said, numbers are numbers, we respect them 🫡)

📚 REFERENCES 📚

🎀 SEE YOU LATER 🎀

and that's the whole page bestie!! this was rabema_build_gold_standard version 1.2.14, section 1 of the manual 💖 (the date on the footer got cut off at [t, so we're just gonna send her off with love). go build that gold standard, you're gonna slay, mwah 🌈💅✨

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