Make truncating the histogram optional in CollectInsertSizeMetrics #1779
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@yfarjoun could you review this small PR? |
yfarjoun
suggested changes
Feb 27, 2022
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Thanks @takutosato for this enhancement.
A few requests to make the changes more inline with Picard "philosophy"....
| import htsjdk.samtools.SAMFileWriter; | ||
| import htsjdk.samtools.SAMFileWriterFactory; | ||
| import htsjdk.samtools.SAMRecordSetBuilder; | ||
| import htsjdk.samtools.*; |
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please bring back the individual imports
src/test/java/picard/analysis/CollectInsertSizeMetricsTest.java
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| setBuilder.addPair("outlierRead", 0, start, start + outlierInsertSize - readLength, | ||
| false, false, cigar, cigar, false, true, 60); | ||
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| final SAMFileWriter writer = new SAMFileWriterFactory().setCreateIndex(true).makeBAMWriter(setBuilder.getHeader(), false, testSamFile); |
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use try-with-resources here.
| } | ||
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| // Add an outlier | ||
| int outlierInsertSize = 2000; |
| final int maxInsertSize = 400; | ||
| int i = 0; | ||
| int start = 1000; | ||
| String cigar = readLength + "M"; |
| final int minInsertSize = 100; | ||
| final int maxInsertSize = 400; | ||
| int i = 0; | ||
| int start = 1000; |
| final MetricsFile<InsertSizeMetrics, Comparable<?>> output = new MetricsFile<>(); | ||
| output.read(new FileReader(outfile)); | ||
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| Assert.assertEquals(output.getAllHistograms().get(0).get(outlierInsertSize).getValue(), 1.0); |
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run with other argument to show that this argument makes a difference
| setBuilder.setReadLength(readLength); | ||
| final int minInsertSize = 100; | ||
| final int maxInsertSize = 400; | ||
| int i = 0; |
Co-authored-by: Yossi Farjoun <farjoun@broadinstitute.org>
Co-authored-by: Yossi Farjoun <farjoun@broadinstitute.org>
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@takutosato are you able to complete the last of @yfarjoun 's requested changes for this PR? |
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From what I can see this looks almost ready to go? @takutosato would you like me to take a look at the last few changes requested or do you have some time to do it? |
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Description
It's true that you can adjust some existing parameters to turn off truncating, but sometimes it's easier to just turn it off and the user should have that option.
Checklist (never delete this)
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