Troubleshooting

Troubleshooting

"Unable to detect the tool type from the provided input"

The auto-detection heuristic did not recognise any known signature in the first 4 096 bytes. Use the explicit ToolType overload instead, or verify that the file is not corrupted or empty.

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Sequence contains many N characters

When a parser cannot find an explicit nucleotide label for a position, it inserts 'N' as a placeholder. This is expected for positions that appear in interaction lines but not in the sequence header. A WARN log entry is emitted for each such case.

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IllegalStateException: mark/reset not supported

Wrap your InputStream in new BufferedInputStream(...) before passing it to any auto-detecting method:

try (BufferedInputStream bis = new BufferedInputStream(new FileInputStream(myFile))) {
    String result = unifier.process(bis, true);
}

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Wrong pairs or missing interactions

• Make sure you passed the correct ToolType. Mismatched tool types can cause a grammar mismatch and silently produce incomplete structures or throw ParseException.
• Check WARN-level log output: skipped pairs are always reported with a reason. See Logging for how to enable WARN output.

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Numbers don't match expected output

Positions in the Pair model are zero-based. The BPSEQ output is 1-based (the exporter adds 1 when printing). If you read positions from Pair.getPos1() / getPos2() directly, add 1 to compare with BPSEQ output.

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