Accept MAF input#86
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Adds a BlockReader abstraction that sniffs MAF/TAF on open, reads the right header, and dispatches subsequent block reads -- including the alignment_link_adjacent call that MAF input needs for cross-block coordinate continuity. Migrates each tool's read loop to it, so users no longer need to pipe through 'taffy view' to consume a MAF. stats -b (sequence intervals) is no longer rejected on MAF input. Output formats per tool are unchanged for now -- pass 2 will make output mirror input where it makes sense. Adds unit tests for BlockReader plus a per-tool regression test that diffs direct-MAF invocation against 'taffy view -i x.maf | tool'. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
Each migrated tool's `block_reader_open == NULL` path now releases the LI handle, the input FILE*, and (where applicable) the LW output writer before returning 1. Previously these leaked until process exit -- not observable in practice but worth fixing for hygiene. Also drops the redundant `if (r->header != NULL)` guard in block_reader_destruct since tag_destruct accepts NULL. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
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Adds abstraction layer over maf/taf reading, and use it in the various tools. Now you can run all the taffy tools on MAF inputs, rather than needing to pipe through taffy view. Output remains TAF by default (with some tools having maf output toggles).