Add a native GATK implementation for 2bit references, and remove the dependency on the ADAM library #8606
Conversation
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
|
Github actions tests reported job failures from actions build 7138120890
|
…dependency on the ADAM library
droazen
force-pushed
the
dr_remove_adam_dependency
branch
from
84aa56a to
504109c
Compare
droazen
commented
Dec 8, 2023
| private static Int2ObjectMap<Insert> consolidateInserts(final List<Insert> inserts, final IntList offsets) { | ||
| final int size = inserts.size(); | ||
| if (size == 0) { | ||
| return Int2ObjectMaps.emptyMap(); | ||
| return (Int2ObjectMap<Insert>)Int2ObjectMaps.EMPTY_MAP; |
There was a problem hiding this comment.
Pin fastutil to 7.0.13 and get rid of this
droazen
commented
Dec 8, 2023
| * @param rule Whether to merge adjacent intervals, or just overlapping intervals | ||
| * @return A new list of merged disjoint intervals, sorted by start position | ||
| */ | ||
| public static List<SimpleInterval> sortAndMergeIntervals(final List<SimpleInterval> raw, final IntervalMergingRule rule) { |
There was a problem hiding this comment.
Strongly consider adding a check enforcing a single-contig restriction
droazen
commented
Dec 8, 2023
| // TTCCAttgTTGTGATTTTGTGctaTTAAAATGATCAAAACANNNCCCTTAAAAATCTTAT | ||
| // TCTAACCTCTCAANNNCTTTTAAAaatgaNNNATTTCAGTACAGTCGGATGCATCTGTAA | ||
| // AAGATAAAAAtaTaACATTGATTAGTTTgCAAAAATAATTGTTTGACCCCAGTTAAGNga | ||
| private static final GATKPath maskedTwoBitTest = new GATKPath(packageRootTestDir + "utils/reference/masked.2bit"); |
There was a problem hiding this comment.
Make a note of how this was created
droazen
commented
Dec 8, 2023
|
|
||
| try { | ||
| // Load the raw contents of the 2bit file into a read-only in-memory ByteBuffer | ||
| rawBytes = ByteBuffer.wrap(ByteStreams.toByteArray(BucketUtils.openFile(referencePath.getRawInputString()))).asReadOnlyBuffer(); |
There was a problem hiding this comment.
GATKPath.getInputStream()
droazen
commented
Dec 8, 2023
| // The total number of sequences in the file | ||
| private int sequenceCount; | ||
|
|
||
| private LinkedHashMap<String, TwoBitSequenceRecord> sequenceRecords; |
There was a problem hiding this comment.
Add a comment that the order does in fact matter here
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
No description provided.