Add Batch Controls Mode supporting fixed variant coordinates and customizable variant types, VAF, and indel sizes

Support optional gzip compression for FASTQ output files to reduce size

Use conditional native st.download_button for files larger than 200MB to bypass Streamlit's static size limit

Use target=_blank and rel=noopener in download links to bypass iframe restrictions

Restore path strings in results dict to fix KeyError, and make IGV browser checkbox-optional

Optimize memory usage by using zero-memory direct HTML links for output downloads

Enable extraction and downloading of synthetic paired-end FASTQ files

Add window-based variant placement strategy for Direct Probe Coordinates mode

Use exact amplicon coordinates as read length in PCR amplicon mode

Fix TypeError when fully_covered_bed_path is None

Support hg19 reference genome and PCR Amplicon sequencing style

Support variant generation in Direct BED Mode (ignoring MANE transcripts) and improve dynamic tracks in igv.js

Support loading MANE transcripts in igv.js, add toggles for CDS/intron/off-target variants, and add MANE transcripts download

Copy static files to both CWD static and script static paths to resolve 404

Add path diagnostics to Debug Info sidebar

Fix NameError by initializing uploaded_bed from session state before sidebar

Update Dockerfile to copy .streamlit config and update src/ files with customized app code

Create packages.txt

Create requirements.txt

Create pipeline.py

Update src/streamlit_app.py

Duplicate from streamlit/streamlit-template-space