Fix read length plot for limited variation data.#2085
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daviesrob
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Jul 26, 2024
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Looks like a good fix for the read length plot, although in testing I found it's still possible to break plot-bamstats elsewhere by not giving it much data. E.g.:
mkdir /tmp/stats
./samtools stats test/dat/view.002.sam > /tmp/view.002.stats
./misc/plot-bamstats -p /tmp/stats/view.002 /tmp/view.002.stats
Warning: empty x range [1:1], adjusting to [0.99:1.01]
Warning: empty x range [1:1], adjusting to [0.99:1.01]
Warning: empty x range [2:2], adjusting to [1.98:2.02]
plot '-' smooth csplines with lines lc 1 title 'First fragments'
^
"/tmp/stats/view.002-gc-content.gp", line 12: Can't calculate splines, need at least 3 points
The command exited with non-zero status 256:
gnuplot /tmp/stats/view.002-gc-content.gp
This may be something to look at in the future.
Meanwhile, #2068 (comment) notes that the read length plot doesn't appear on the html page. It doesn't look like it should be too hard to add...
Added read-length to html page. Changed file suffix from read_length to read-length to match the other file names.
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Fixes #2068 where the limited length variations were causing the x range to be wrong. Some other changes to quiet warnings about y ranges.