WHAM(1)

🌸 NAME 🌸

okay bestie, meet wham — Wisconsin's High-Throughput Alignment Method 💖 like it literally says that on the tin, no cap.

---

✨ DESCRIPTION ✨

📋 Usage

here's the whole vibe of how you call her, exactly as written, don't @ me:

wham [options]* {<readfile> | -1 <m1file> -2 <m2file>} <basepath>
<output> <readfile>         comma-separated list of files containing unpaired reads
<m1file>           comma-separated list of files containing upstream mates
<m2file>           comma-separated list of files containing downstream mates
<basepath>         write wham data to files with this dir/basename
<output>           file to write alignments to

so like, every one of those placeholders matters:

• <readfile> — a comma-separated list of files holding unpaired reads 🍓
• <m1file> — a comma-separated list of files holding upstream mates
• <m2file> — a comma-separated list of files holding downstream mates
• <basepath> — write wham data to files with this dir/basename 🎀
• <output> — the file where the alignments go 🦋

---

🎀 Input options

• -l <int> — use the first <int> bases in each read. short king energy, only the beginning counts 💅

---

🔥 Alignment options

• -v <int> — specify the max number of errors allowed in a reported alignment. yes, a cap, bestie 🙈
• -g, --gap <int> — specify the max number of gaps in a reported alignment.
• -e, --maqerr <int> — max sum of mismatch quals across the alignment. it's giving ✨quality math✨
• --nofw, --norc — do not align to the forward / reverse-complement ref strand.
• --nofr, --norf — do not align to the mate1/mate2 strand: fw/rev, rev/fw.
• -I, --minins <int> — minimum insert size for paired-end alignment (default: 0).
• -X, --maxins <int> — maximum insert size for paired-end alignment (default: 250).

---

👑 Reporting options

• -k <int> — report up to <int> valid alignemtns per read (default: 1).
• -a, --all — report all valid alignments per read. greedy girl, we respect it 👑
• --best — reprot valid alignments in a sorted order of quality.
• -m <int> — discard reads with more than <int> valid alignmetns. bye bye ambiguity 💀

---

🦋 Output options

• -S, --sam — write alignment in SAM format.
• --al <fname> — write aligned reads/pairs to file(s) <fname>.
• --un <fname> — write unaligned reads/pairs to file(s) <fname>.

---

⭐ Performance options

• -t <int> — specify the number of threads. more threads, more main character energy 🌈
• --nocat — do not concatenate results from various threads.
• --step <int> — specify the number of indexes that fit into memory.

---

💜 Other options

• --version — print version information.
• -h, --help — print this usage message. the classic 🫶

---

🫶 AUTHOR 🫶

This manpage was written by Nilesh Patra for the Debian distribution and can be used for any other usage of the program. periodt 💖

---

and that's the whole thing, bestie — wham 0.1.5, dated February 2021, dropping out of the User Commands section like the icon it is ✨🎀💅 slay, read the manpage, stay hydrated 🦋🌸