Update README.md to reflect current overlaps.tsv output format

[Copilot]

FEDRANN now outputs a single overlaps.tsv file containing all overlap information, rather than separate metadata.tsv and overlaps.tsv files with index-based references.

Changes

• Output section: Removed metadata.tsv reference, updated overlaps.tsv description to reflect it contains complete overlap data
• overlaps.tsv example: Replaced old format (index, read_name, strand) with current format showing actual overlap records:

  query_name	query_orientation	target_name	target_orientation	neighbor_rank	distance
  c2924806-d5c6-4564-b31a-c701c0226fbc	+	7e3d8f0e-fcf0-4073-ad6b-6d742245f29b	+	1	0.6606640366100363
  

• Column descriptions: Added documentation for query_name, query_orientation, target_name, target_orientation, neighbor_rank, and distance
• Program flowchart: Updated OUTPUT FILES section to show only overlaps.tsv and feature_matrix.npz

The new format directly provides sequence names and orientations for each overlap pair, eliminating the need for index lookups.

Original prompt

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This section details on the original issue you should resolve

<issue_title>Update README.md</issue_title>
<issue_description>Fedrann now outputs only overlaps.tsv without metadata.tsv. Below is an example:

query_name	query_orientation	target_name	target_orientation	neighbor_rank	distance
c2924806-d5c6-4564-b31a-c701c0226fbc	+	7e3d8f0e-fcf0-4073-ad6b-6d742245f29b	+	1	0.6606640366100363
c2924806-d5c6-4564-b31a-c701c0226fbc	+	dd1acbc0-f219-4701-b1eb-00b9850d3d9e	-	2	0.6690033249609217
c2924806-d5c6-4564-b31a-c701c0226fbc	+	9b58f527-6e4d-4005-92cb-4863b6d42229	+	3	0.7207873470869667
c2924806-d5c6-4564-b31a-c701c0226fbc	+	932c6e73-e5d9-4bbe-b88f-e4babfc043a1	-	4	0.7347354015555427
c2924806-d5c6-4564-b31a-c701c0226fbc	+	416c786a-11f1-487f-99cc-830a40ee1c6c	-	5	0.7421239213106542
c2924806-d5c6-4564-b31a-c701c0226fbc	+	99640d4e-d299-414c-ade3-ebe567b4d1ef	+	6	0.7520030538483087
c2924806-d5c6-4564-b31a-c701c0226fbc	+	ffdda27d-9d97-4d01-8e61-8a6e281e0f69	+	7	0.7670946853284661
c2924806-d5c6-4564-b31a-c701c0226fbc	+	2e92fbd0-4577-405f-a0c4-5123179a9e78	+	8	0.7840616303663797

Update README.md accordingly. </issue_description>

Comments on the Issue (you are @copilot in this section)

• Fixes Update README.md #17

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