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Issue #7159 Create tool for producing genomic regions (as a BED file) #8942

Merged
merged 49 commits into from
Aug 29, 2024
Merged

Issue #7159 Create tool for producing genomic regions (as a BED file) #8942

merged 49 commits into from
Aug 29, 2024

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sanashah007
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Converts GTF files to BED file format with an option for gene or transcript level processing and an option to only use transcripts with basic tag

@sanashah007
Initial commit and basic code to read gtf
4436f85
@sanashah007
add: code to write to bed & integration test
f4a84be
@sanashah007
fix: make getAllFeatures public and use the nesting of features to ge…
8139a96 
…t to transcripts
@sanashah007
add: filtering transcripts by basic tag
c35c829
@sanashah007
add: sorts by contig and start (need to fix - sorting lexicographically)
0366e35
@sanashah007
fix: now sorts by contig then start & output is correct
d2323ff
@sanashah007
fix: make dictionary an arg
9b6e27a
@sanashah007
add: comments + simplified CompareGtfInfo
bd5a019
@sanashah007
refactor: apply method
0ef5498 
test: add separate tests for gene and transcript
@sanashah007
refactor: onTraversalSuccess and writeToBed
cdbe336
@sanashah007
add: more tests
924216b
@sanashah007
fix: test files in correct dir pt1. (files are too large)
2d80fa0
@sanashah007
fix: test files in correct dir pt2.
db3a24e
@sanashah007
add: compareFiles and ground truth bed files
7dc019d
@sanashah007
fix: runGtfToBed assert
4b35136
@sanashah007
add: comments to GtfToBed
799fee5
@sanashah007
fix: error handling for different versions of gtf and dictionary
f8be0b2
@sanashah007
fix: edited some bad conventions
3d2570a
@sanashah007
fix: remove spaces from input file fullName
1dec98b
@sanashah007
add: gtf file with MYT1L and MAPK1
3d976f9
@sanashah007
add: many transcripts unit test and refactoring
22a99af
@sanashah007
add: tiebreaker sorting by id
e1835c8
@sanashah007
add: make sort by basic optional
2aae3ae
@sanashah007
add: html doc comment
87e10bc
@droazen droazen requested a review from jamesemery August 5, 2024 19:31
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droazen commented Aug 5, 2024

@jamesemery please review

@sanashah007
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@jamesemery Thanks for the comments, I am ready for a re-review.

jamesemery
jamesemery requested changes Aug 16, 2024
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A few relatively minor comments and one potential bug. Its getting close to being able to merge

src/test/java/org/broadinstitute/hellbender/tools/walkers/conversion/ConversionTestUtils.java Outdated Show resolved Hide resolved
src/test/java/org/broadinstitute/hellbender/tools/walkers/conversion/ConversionTestUtils.java Outdated Show resolved Hide resolved
src/main/java/org/broadinstitute/hellbender/tools/walkers/conversion/GtfInfo.java Show resolved Hide resolved
src/main/java/org/broadinstitute/hellbender/tools/walkers/conversion/GtfToBed.java Outdated Show resolved Hide resolved
src/main/java/org/broadinstitute/hellbender/tools/walkers/conversion/GtfToBed.java Outdated Show resolved Hide resolved
src/test/java/org/broadinstitute/hellbender/tools/walkers/conversion/ConversionTestUtils.java Outdated Show resolved Hide resolved
src/main/java/org/broadinstitute/hellbender/tools/walkers/conversion/GtfToBed.java Outdated Show resolved Hide resolved
src/main/java/org/broadinstitute/hellbender/tools/walkers/conversion/GtfToBed.java Outdated Show resolved Hide resolved
jamesemery
jamesemery approved these changes Aug 29, 2024
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To my eye this looks good. Two very minor comments and then once those are good feel free to merge.

src/main/java/org/broadinstitute/hellbender/tools/walkers/conversion/GtfToBed.java Outdated Show resolved Hide resolved
src/main/java/org/broadinstitute/hellbender/tools/walkers/conversion/GtfToBed.java Outdated Show resolved Hide resolved
@sanashah007 sanashah007 merged commit 3c1430d into master Aug 29, 2024
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@sanashah007 sanashah007 deleted the ss_issue7159_gtfToBed branch August 29, 2024 20:15
@kockan kockan mentioned this pull request Aug 29, 2024
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@lbergelson lbergelson lbergelson left review comments

@jamesemery jamesemery jamesemery approved these changes

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@sanashah007 @droazen @lbergelson @jamesemery @LeeTL1220