export2sam-pl

name	export2sam-pl
description	Use when converting legacy Illumina GERALD export files into SAM for downstream alignment analysis.
disable-model-invocation	true
user-invocable	true

export2sam-pl

Quick Start

• Command: export2sam.pl --read1=lane1_export.txt [options] > alignments.sam
• Local executable: /home/vimalinx/miniforge3/envs/bio/bin/export2sam.pl
• Reference: See references/help.md

When To Use This Tool

• Convert Illumina GERALD / CASAVA export files into standard SAM.
• Handle single-end or paired-end export files with --read1 and optional --read2.
• Keep failed-purity-filter reads with --nofilter when you need full raw export coverage.
• Interpret older Solexa log-odds qualities correctly with --qlogodds.

Common Patterns

# 1) Convert a single-end export file
export2sam.pl \
  --read1=s_1_export.txt > alignments.sam

# 2) Convert paired-end export files
export2sam.pl \
  --read1=s_1_1_export.txt \
  --read2=s_1_2_export.txt > paired.sam

# 3) Include failed-filter reads and interpret old log-odds qualities
export2sam.pl \
  --read1=s_1_export.txt.gz \
  --nofilter \
  --qlogodds > legacy.sam

Recommended Workflow

1. Confirm the inputs are GERALD export files and not FASTQ, ELAND, or ordinary SAM.
2. Supply --read1 first, then add --read2 only when the files form a true read pair.
3. Decide whether the run predates OLB/Pipeline 1.3; only then enable --qlogodds.
4. Convert, then inspect flags and optional fields before folding the output into later BAM-based steps.

Guardrails

• --read1 is mandatory; this script does not do anything useful without it.
• --nofilter changes the dataset by retaining reads that failed the basecaller purity filter; those reads are marked with SAM flag 0x0200.
• --qlogodds is only for old Solexa-style export qualities; do not enable it on newer phred-style exports.
• Gzipped inputs are supported via .gz, and - can be used for stdin input, but this is still a legacy GERALD-specific converter rather than a general FASTQ-to-SAM tool.