How do I install the Propmapped skill?

Run npx skillmds add vimalinx/propmapped in your terminal (requires Node.js), paste this page's agent-chat prompt into Claude, Cursor, or any MCP-connected agent, or download the SKILL.md file and copy it into your agent's skills directory.

Is Propmapped safe to use?

This skill has not completed SkillMD's automated safety review yet. Capability flags: docs only. SkillMD never runs a skill's scripts for you; review the SKILL.md before installing.

Which AI agents work with Propmapped?

This skill is tagged as working with Claude Code, Claude.ai, OpenAI Codex. SKILL.md is an open format, so most agents that read a skills directory can load it too.

Is Propmapped free to use?

Yes. Installing skills from SkillMD is free, and the skill stays under its author's original license.

Who published Propmapped?

vimalinx (@vimalinx) published this skill. Their other Agent Skills are listed on their SkillMD profile.

Propmapped by vimalinx — Agent Skill

Name: Propmapped
Rating: 4.666666666666667 (3 reviews)
Author: vimalinx

File contents

propmapped

propmapped is a compact alignment-summary binary that reports mapped fractions for reads or fragments. In local tests it wrote results only when -o was provided, using a simple comma-separated summary line.

Quick Start

Command: propmapped -i <input.sam|input.bam> [-o <out.csv>] [-f] [-p]
Local executable: /home/vimalinx/miniforge3/envs/bio/bin/propmapped
Scope: reports mapping proportion only; does not modify alignments

When To Use This Tool

Calculating the proportion of mapped reads or fragments from alignment files in SAM or BAM format. Supports both single-end and paired-end reads, with options to count fragments as pairs or filter for properly paired reads only.

Common Patterns

# 1) Single-end mapping fraction
propmapped -i aln.sam -o aln.mappability.csv

# 2) Count paired-end fragments instead of reads
propmapped -i pairs.sam -f -o pairs.fragments.csv

# 3) Restrict paired-end counting to properly paired fragments
propmapped -i pairs.sam -f -p -o pairs.proper.csv

Recommended Workflow

Start from a finished SAM/BAM file, not a stream that is still being written.
Decide whether your unit of interest is reads or fragments before adding -f.
Use -p only when proper-pair status is meaningful for your dataset.
Save the result with -o and parse the emitted CSV line downstream.

Guardrails

Input file must be in SAM or BAM format (required -i argument)
The -f and -p options are only applicable for paired-end reads
-h, --help, and --version are all unrecognized options, but the binary still prints its usage banner and embedded version string (propMapped v2.1.1).
The usage text contains a typo: it advertises ./prommapped, while the actual executable is propmapped.
In local tests, propmapped -i file.sam wrote nothing to stdout; the useful output appeared only after adding -o.
A single-end smoke test produced /path/min.sam,2,1,0.500000, indicating the output fields are path,total,mapped,fraction.
A paired-end -f -p test on one proper pair produced /path/pairs.sam,1,1,1.000000, confirming that -f collapses to fragment counts.

---name: propmappeddescription: Use when you need to calculate the proportion of mapped reads or fragments from SAM/BAM alignment files to assess mapping quality and success rates.--- # propmapped `propmapped` is a compact alignment-summary binary that reports mapped fractions for reads or fragments. In local tests it wrote results only when `-o` was provided, using a simple comma-separated summary line. ## Quick Start - **Command:** `propmapped -i <input.sam|input.bam> [-o <out.csv>] [-f] [-p]` - **Local executable:** `/home/vimalinx/miniforge3/envs/bio/bin/propmapped` - **Scope:** reports mapping proportion only; does not modify alignments ## When To Use This Tool Calculating the proportion of mapped reads or fragments from alignment files in SAM or BAM format. Supports both single-end and paired-end reads, with options to count fragments as pairs or filter for properly paired reads only. ## Common Patterns ```bash # 1) Single-end mapping fraction propmapped -i aln.sam -o aln.mappability.csv ``` ```bash # 2) Count paired-end fragments instead of reads propmapped -i pairs.sam -f -o pairs.fragments.csv ``` ```bash # 3) Restrict paired-end counting to properly paired fragments propmapped -i pairs.sam -f -p -o pairs.proper.csv ``` ## Recommended Workflow 1. Start from a finished SAM/BAM file, not a stream that is still being written. 2. Decide whether your unit of interest is reads or fragments before adding `-f`. 3. Use `-p` only when proper-pair status is meaningful for your dataset. 4. Save the result with `-o` and parse the emitted CSV line downstream. ## Guardrails - Input file must be in SAM or BAM format (required `-i` argument) - The `-f` and `-p` options are only applicable for paired-end reads - `-h`, `--help`, and `--version` are all unrecognized options, but the binary still prints its usage banner and embedded version string (`propMapped v2.1.1`). - The usage text contains a typo: it advertises `./prommapped`, while the actual executable is `propmapped`. - In local tests, `propmapped -i file.sam` wrote nothing to stdout; the useful output appeared only after adding `-o`. - A single-end smoke test produced `/path/min.sam,2,1,0.500000`, indicating the output fields are `path,total,mapped,fraction`. - A paired-end `-f -p` test on one proper pair produced `/path/pairs.sam,1,1,1.000000`, confirming that `-f` collapses to fragment counts.

Frequently asked questions