fix: Handle trailing tabs and quoted fields in Agilent Gen5 parser#1241
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stephenworlow
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Jul 14, 2026
Some Gen5 exports (e.g. Synergy H1) produce files with trailing tabs on every line, leading tabs on data sections, and quoted fields containing commas. This caused multiple parse failures: header DataFrame had extra rows, section names were quoted, kinetic/results data had shifted columns, and non-UTF-8 encoding wasn't detected. Fixes: - Add chardet encoding detection for non-UTF-8 files - Strip trailing tabs from all lines at read time - Strip quotes from procedure detail lines in DeviceControlData - Extract section names from first non-empty tab field (handles leading tabs) - Detect and strip extra leading tab from data sections - Merge section data when a blank line separates header from content Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
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stephenworlow
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Summary
°encoded as 0xB0 in Windows-1252)"Optics: Bottom, Gain: 75") by stripping quotes before parsingLayout\n\n<data>)These issues all originate from a specific Gen5 export variant (Synergy H1 reader) that pads every line with trailing tabs, prepends an extra tab to data rows, and quotes fields containing commas.
Test plan
PR391_020 plate1.txt) parses successfully with 96 well documents🤖 Generated with Claude Code