Split At Intron

# 2) Minimal illustrative event stream
cat <<'EOF' | split-at-intron
index	1
score	95
start	1000
strand	plus
match	80
genomic-ins	120
match	50
end	0
EOF

Recommended Workflow

1. Make sure the upstream step emits the expected tab-separated tag/value stream with fields like index, score, start, strand, match, genomic-ins, and end.
2. Pipe that stream into split-at-intron; the tool does not take ordinary interval files or command-line arguments.
3. Inspect the emitted interval list to confirm that large genomic insertions were split into separate segments.
4. Feed the resulting coordinate strings only into downstream code that understands this EDirect-style output format.

Guardrails

• This tool reads stdin and expects a very specific Entrez Direct tag/value event stream; it is not a generic intron splitter for BED, GFF, or FASTA.
• In the bundled script, only genomic-ins events of length >= 30 trigger a split; shorter insertions are absorbed into the current span.
• The output format is a compact coordinate representation, not a standard BED file.
• If the upstream stream is missing tags such as start, strand, or end, the output will be incomplete or meaningless.