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When thisHit#length is equivalent and thisHit#percentID is higher than bestHit, replace bestHit with thisHit
Consider ContaminantHit#percentID in ContaminentFinder.java
Increase the default memory allocation to 512MB Add a --memory option to allow the user to increase the base memory allocation without messing around with --threads Add the ExitOnOutOfMemoryError option to the JVM launch so that OOM instances don't hang. Fixes s-andrews#86 Fixes s-andrews#88 Fixes s-andrews#75
Used the colours from https://davidmathlogic.com/colorblind/
Update SVG branch to current
Bring SVG into line
Bring SVG output into main
Some of the larger illumina flowcells might now be exceeding the 1000 tile limit (largest we've seen is 936 but we don't run all possible flowcells) so let's give this some headroom.
Also fix the truncation at 50bp unless this is overidden. Fixes s-andrews#114
Using probeContentType is just too fragile - it breaks everywhere except linux. Bump version to 0.12.1
Add htsjdk to build.xml
Add perl install instructions to main install.txt
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I merged in updates on master to the cram branch as of May 2025 and a minor fix. It worked for my organization's crams so I did not test further.