How do I install the Interpolate Sam Pl skill?

Run npx skillmds add vimalinx/interpolate-sam-pl 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 Interpolate Sam Pl 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 Interpolate Sam Pl?

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 Interpolate Sam Pl free to use?

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

Who published Interpolate Sam Pl?

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

Interpolate Sam Pl by vimalinx — Agent Skill

Name: Interpolate Sam Pl
Rating: 4.2 (5 reviews)
Author: vimalinx

File contents

interpolate-sam-pl

Quick Start

Command: interpolate_sam.pl sorted.sam > interpolated.txt
Local executable: /home/vimalinx/miniforge3/envs/bio/bin/interpolate_sam.pl
Reference: See references/help.md

When To Use This Tool

Turn a sorted SAM file into an interpolated base-by-base coverage trace.
Count bases spanned between paired ends rather than only piling up aligned read sequence.
Generate simple per-position depth summaries from older MAQ-style SAM workflows.
Produce a lightweight text coverage profile without launching a full coverage toolkit.

Common Patterns

# 1) Generate interpolated per-base counts from a sorted SAM file
interpolate_sam.pl \
  alignments.sorted.sam > interpolated.txt

# 2) Save per-contig coverage blocks for downstream plotting
interpolate_sam.pl \
  alignments.sorted.sam > coverage.blocks.txt

# 3) Inspect the first region header and counts
interpolate_sam.pl \
  alignments.sorted.sam | head -n 40

Recommended Workflow

Start from a SAM file that is already sorted in the order expected by the script.
Confirm the reference names and CIGAR strings match the assumptions documented in the source comments.
Generate the interpolated count output, then inspect the #RNAME block headers and early counts for sanity.
Use the output as a lightweight diagnostic or plotting input rather than as a drop-in replacement for modern pileup/depth tools.

Guardrails

This script expects a SAM filename as its first positional argument; --help and --version are treated as missing-file names and error out.
The input SAM must be sorted.
It expects simple CIGAR operations (M, I, and D) and a colon-delimited RNAME format such as chromosome:NCBI36:18:1:76117153:1.
The source comments note an MAQ-specific assumption that flag 0x0010 marks the second read in paired-end data, so validate behavior before using it on arbitrary modern SAM files.

---name: interpolate-sam-pldescription: Use when deriving interpolated per-base coverage counts from a sorted SAM file, especially across paired-end inserts.--- # interpolate-sam-pl ## Quick Start - **Command:** `interpolate_sam.pl sorted.sam > interpolated.txt` - **Local executable:** `/home/vimalinx/miniforge3/envs/bio/bin/interpolate_sam.pl` - **Reference:** See [references/help.md](references/help.md) ## When To Use This Tool - Turn a sorted SAM file into an interpolated base-by-base coverage trace. - Count bases spanned between paired ends rather than only piling up aligned read sequence. - Generate simple per-position depth summaries from older MAQ-style SAM workflows. - Produce a lightweight text coverage profile without launching a full coverage toolkit. ## Common Patterns ```bash # 1) Generate interpolated per-base counts from a sorted SAM file interpolate_sam.pl \ alignments.sorted.sam > interpolated.txt ``` ```bash # 2) Save per-contig coverage blocks for downstream plotting interpolate_sam.pl \ alignments.sorted.sam > coverage.blocks.txt ``` ```bash # 3) Inspect the first region header and counts interpolate_sam.pl \ alignments.sorted.sam | head -n 40 ``` ## Recommended Workflow 1. Start from a SAM file that is already sorted in the order expected by the script. 2. Confirm the reference names and CIGAR strings match the assumptions documented in the source comments. 3. Generate the interpolated count output, then inspect the `#RNAME` block headers and early counts for sanity. 4. Use the output as a lightweight diagnostic or plotting input rather than as a drop-in replacement for modern pileup/depth tools. ## Guardrails - This script expects a SAM filename as its first positional argument; `--help` and `--version` are treated as missing-file names and error out. - The input SAM must be sorted. - It expects simple CIGAR operations (`M`, `I`, and `D`) and a colon-delimited `RNAME` format such as `chromosome:NCBI36:18:1:76117153:1`. - The source comments note an MAQ-specific assumption that flag `0x0010` marks the second read in paired-end data, so validate behavior before using it on arbitrary modern SAM files.

Frequently asked questions