propmapped

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

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

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.