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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 added 24 commits July 10, 2024 10:09
@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.

@sanashah007 sanashah007 requested a review from jamesemery August 13, 2024 21:29
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
@sanashah007 sanashah007 requested a review from jamesemery August 27, 2024 18:13
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