repair

name	repair
description	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.
disable-model-invocation	true
user-invocable	true

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

1. 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.