vcf-fix-newlines

name	vcf-fix-newlines
description	Use when VCF files have inconsistent or non-native newline characters and need normalization before downstream processing.
disable-model-invocation	true
user-invocable	true

vcf-fix-newlines

Quick Start

• Command: vcf-fix-newlines [OPTIONS] [file.vcf|file.vcf.gz] > out.vcf
• Local executable: /home/vimalinx/miniforge3/envs/bio/bin/vcf-fix-newlines
• Full reference: See references/help.md

When To Use This Tool

• Normalize a VCF transferred from Windows or legacy systems before downstream parsing.
• Detect whether a file's newline style matches the current platform with -i.
• Clean a plain VCF or .vcf.gz before feeding it into stricter tooling.
• Repair line-ending issues without changing the variant content itself.

Common Patterns

# 1) Report the source newline style only
vcf-fix-newlines -i file.vcf

# 2) Normalize a gzipped VCF into a plain-text output VCF
vcf-fix-newlines file.vcf.gz > fixed.vcf

# 3) Normalize a streamed VCF
cat file.vcf | vcf-fix-newlines > fixed.vcf

Recommended Workflow

1. Probe first with -i if you are not sure whether newline normalization is actually needed.
2. Convert into a new output file instead of trying to overwrite the source.
3. Recompress and reindex afterward if the downstream pipeline expects .vcf.gz plus tabix.
4. Validate the resulting VCF with a parser once the line endings are fixed.

Guardrails

• On this Linux machine, if the input already uses \n, the tool prints No conversion needed. and exits without echoing the file to stdout; do not use it as a transparent pass-through stage.
• .vcf.gz input relies on gunzip -c being available.
• -i only reports the detected platform / newline style; it does not emit the converted file.
• This script determines newline style from an initial sample of the file and errors if the format is too inconsistent to classify cleanly.
• The tool writes normalized content to stdout, so always redirect it to a new file.