How do I install the Repair skill?

Run npx skillmds@latest add vimalinx/repair 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 Repair safe to use?

This skill has not completed SkillMD's automated safety review yet. Independent scanners report: SkillSpector: PASS, Skill Scanner: PASS. Capability flags: docs only. SkillMD never runs a skill's scripts for you; review the SKILL.md before installing.

Which AI agents work with Repair?

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 Repair free to use?

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

Who published Repair?

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

Repair by vimalinx — Agent Skill

Name: Repair
Rating: 4.2 (5 reviews)
Author: vimalinx

File contents

repair

repair is a pair-order repairer for SAM/BAM. It rewrites output as BAM, optionally adds dummy mates for singletons/unpaired reads, and is designed to make the output acceptable to featureCounts.

Quick Start

Command: repair -i input.bam -o output.bam
Local executable: /home/vimalinx/miniforge3/envs/bio/bin/repair
SAM input switch: add -S when the input is SAM rather than BAM

When To Use This Tool

Reordering paired-end reads so mates from the same pair appear next to each other in the output
Adding dummy reads for singleton reads that lack a pair, making output compatible with featureCounts
Converting SAM to BAM while repairing pair order
Processing BAM/SAM files to ensure proper paired-read alignment for downstream counting tools

Common Patterns

# 1) Repair a BAM file with default dummy-read behavior
repair -i input.bam -o repaired.bam

# 2) Repair SAM input
repair -S -i input.sam -o repaired.bam

# 3) Suppress dummy mates for singleton reads
repair -d -S -i input.sam -o repaired.bam

Recommended Workflow

Decide whether you want featureCounts-compatible dummy mates; if not, add -d.
Use -S explicitly for SAM input and leave it off for BAM input.
Write to a fresh BAM path and inspect the output with samtools view.
Only then pass the repaired BAM into counting or other pair-sensitive downstream tools.

Guardrails

Input and output files must be specified with -i and -o (no defaults)
Output is always BAM format; there is no SAM output option
-h and --help are not clean help flags; they are treated as invalid options and then the program prints its usage banner (repair Version 2.1.1).
In local tests, singleton or unpaired reads caused repair to add dummy mates with sequence N and quality A.
-d really suppresses dummy-read insertion: a singleton SAM stayed singleton in the repaired BAM when this flag was used.
A two-read smoke test with flags 73 and 137 was treated as two unpaired reads and produced one dummy mate for each, so pair interpretation is strict.
The binary's own strings include ERROR: featureCounts does not support counting long paired-end reads., which is a clue that this tool is narrowly targeted at featureCounts compatibility rather than general duplicate/repair logic.

---name: repairdescription: Use when paired-end reads need to be reordered so mates appear consecutively, or when preparing BAM files for featureCounts by adding dummy reads for singletons.---# repair`repair` is a pair-order repairer for SAM/BAM. It rewrites output as BAM, optionally adds dummy mates for singletons/unpaired reads, and is designed to make the output acceptable to `featureCounts`.## Quick Start- **Command:** `repair -i input.bam -o output.bam`- **Local executable:** `/home/vimalinx/miniforge3/envs/bio/bin/repair`- **SAM input switch:** add `-S` when the input is SAM rather than BAM## When To Use This Tool- Reordering paired-end reads so mates from the same pair appear next to each other in the output- Adding dummy reads for singleton reads that lack a pair, making output compatible with featureCounts- Converting SAM to BAM while repairing pair order- Processing BAM/SAM files to ensure proper paired-read alignment for downstream counting tools## Common Patterns```bash# 1) Repair a BAM file with default dummy-read behaviorrepair -i input.bam -o repaired.bam``````bash# 2) Repair SAM inputrepair -S -i input.sam -o repaired.bam``````bash# 3) Suppress dummy mates for singleton readsrepair -d -S -i input.sam -o repaired.bam```## Recommended Workflow1. Decide whether you want featureCounts-compatible dummy mates; if not, add `-d`.2. Use `-S` explicitly for SAM input and leave it off for BAM input.3. Write to a fresh BAM path and inspect the output with `samtools view`.4. Only then pass the repaired BAM into counting or other pair-sensitive downstream tools.## Guardrails- Input and output files must be specified with `-i` and `-o` (no defaults)- Output is always BAM format; there is no SAM output option- `-h` and `--help` are not clean help flags; they are treated as invalid options and then the program prints its usage banner (`repair Version 2.1.1`).- In local tests, singleton or unpaired reads caused `repair` to add dummy mates with sequence `N` and quality `A`.- `-d` really suppresses dummy-read insertion: a singleton SAM stayed singleton in the repaired BAM when this flag was used.- A two-read smoke test with flags `73` and `137` was treated as two unpaired reads and produced one dummy mate for each, so pair interpretation is strict.- The binary's own strings include `ERROR: featureCounts does not support counting long paired-end reads.`, which is a clue that this tool is narrowly targeted at featureCounts compatibility rather than general duplicate/repair logic.

Frequently asked questions

Repair