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Jn compare bam tag values #487

Merged
merged 13 commits into from
Jan 15, 2025
Merged

Jn compare bam tag values #487

merged 13 commits into from
Jan 15, 2025

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jamesnemesh
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Greatly enhanced CompareBAMTagValues to support analysis where BAM files are inexact - tool now emits reads that are discordant between two data sets, reads that are unique to a data set, and a metrics file that contains the tag values in each data set - either for all tag values, or those that are discordant.

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codecov bot commented Jan 14, 2025

Codecov Report

Attention: Patch coverage is 83.23471% with 85 lines in your changes missing coverage. Please review.

Project coverage is 80.76%. Comparing base (32cf96a) to head (7d1ff5f).
Report is 1 commits behind head on master.

Files with missing lines Patch % Lines
...nstitute/dropseqrna/utils/CompareBAMTagValues.java 78.54% 27 Missing and 35 partials ⚠️
...broadinstitute/dropseqrna/utils/DNACompressor.java 92.22% 3 Missing and 4 partials ⚠️
...ls/alignmentcomparison/QueryNameJointIterator.java 78.57% 4 Missing and 2 partials ⚠️
...utils/readiterators/TagValueFilteringIterator.java 73.33% 2 Missing and 2 partials ⚠️
...adinstitute/dropseqrna/utils/ByteArrayWrapper.java 80.00% 0 Missing and 2 partials ⚠️
...a/utils/readiterators/ReadNameCleanupIterator.java 94.28% 0 Missing and 2 partials ⚠️
.../dropseqrna/utils/DNACompressorVaryingLengths.java 0.00% 1 Missing ⚠️
...rna/utils/readiterators/BAMTagCleanupIterator.java 97.43% 0 Missing and 1 partial ⚠️
Additional details and impacted files
@@             Coverage Diff              @@
##             master     #487      +/-   ##
============================================
+ Coverage     80.69%   80.76%   +0.07%     
- Complexity     4702     4812     +110     
============================================
  Files           358      363       +5     
  Lines         20045    20514     +469     
  Branches       3125     3213      +88     
============================================
+ Hits          16175    16569     +394     
- Misses         2607     2641      +34     
- Partials       1263     1304      +41     

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@jamesnemesh jamesnemesh merged commit bf3086b into master Jan 15, 2025
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@jamesnemesh jamesnemesh deleted the jn_CompareBAMTagValues branch January 15, 2025 00:22
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