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uploaded new pattern set
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stephenvrice committed Jan 31, 2025
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8 changes: 5 additions & 3 deletions README.md
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Expand Up @@ -172,7 +172,8 @@ Usage: fuzzort < fuzzion2_hits > sorted_hits

Run `fuzzion2html` to produce an HTML file that provides an attractive display
of hits when opened in a browser such as Google Chrome or Microsoft Edge.
SNPs, indels, and sequencing errors are highlighted in the display.
SNPs, indels, and sequencing errors are highlighted in the display. An example
can be seen [here](https://htmlpreview.github.io/?https://github.com/stjude/fuzzion2/blob/master/test/SJBALL020765_D1_by_pattern.html).

```
Usage: fuzzion2html OPTION ... < fuzzion2_hits > html
Expand Down Expand Up @@ -216,7 +217,8 @@ are divided into two types: "strong+" if at least one read is junction spanning,
In the leftmost column of a display of hits produced by `fuzzion2html`, each hit is
labeled as either "weak," "strong-", or "strong+", or as "dup" if the read pair is a
duplicate of another hit. Furthermore, each read is marked as "+" if it qualifies as
junction spanning and "-" if it does not.
junction spanning and "-" if it does not. As used here, "+" and "-" do not indicate
orientation.

In `fuzzall` output, each sample ID is followed by two numbers in parentheses,
e.g., (24/22), indicating the number of distinct matches (24) and "strong+" matches (22).
Expand Down Expand Up @@ -310,7 +312,7 @@ Coming soon.

## COPYRIGHT

Copyright 2023 St. Jude Children's Research Hospital
Copyright 2025 St. Jude Children's Research Hospital

## LICENSE

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