samtools htsjdk issues - Githubissues

samtools / htsjdk

A Java API for high-throughput sequencing data (HTS) formats.

http://samtools.github.io/htsjdk/

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issues

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Remove requirement that zero length reads need color space or flow si…

#1360 nh13 closed 5 years ago
6
Support VCF v4.3 (read only).

#1359 cmnbroad closed 5 years ago
3
Added name of offending record to error message in SamPairUtil

#1358 yfarjoun closed 5 years ago
2
Improve exception message for unset VCF output type

#1357 clintval closed 5 years ago
2
- make interval operations scale better

#1356 yfarjoun closed 5 years ago
1
Removed redundant readability test in unrollPaths method

#1355 yfarjoun closed 5 years ago
1
- Add a function to calculate the value of the OA tag

#1354 yfarjoun closed 5 years ago
1
Limited API visibility issues around attributes

#1353 heuermh opened 5 years ago
3
Allow BCFCodec subclasses to provide custom version compatibility.

#1352 cmnbroad closed 5 years ago
1
Support writing a CRAI index from CRAMContainerStreamWriter

#1351 tomwhite closed 5 years ago
3
CRAM: is it ok that SamTag doesn't return NM and MD tag for SamRecord?

#1350 PolinaBevad closed 5 years ago
2
CRAM WIP: expand ReferenceContext to include Alignment Start and Span

#1349 jmthibault79 closed 5 years ago
1
WIP: Progress toward Container encapsulation

#1348 jmthibault79 closed 5 years ago
2
CRAM Multi-ref slice indexing is inefficient

#1347 cmnbroad opened 5 years ago
2
Small CRAM refactor: common ExternalEncoding Abstract Base Class

#1346 jmthibault79 closed 5 years ago
1
CRAM tiny refactor: remove CramCompressionRecord.tagIds

#1345 jmthibault79 closed 5 years ago
2
make VariantContextBuilder safer

#1344 yfarjoun closed 5 years ago
7
Add CRAM multi-ref slice index query tests

#1343 cmnbroad closed 2 years ago
2
Remove usages of FakeReferenceSequenceFile

#1342 cmnbroad closed 4 years ago
1
CRAM: revert #1326 and fix tests and comments

#1341 jmthibault79 closed 5 years ago
2
Added fasta.gz write support to FastaReferenceWriterBuilder

#1340 jamesemery closed 5 years ago
4
*CRAMCRAIIndexerTest testMultiRefContainer tests a BAI index

#1339 cmnbroad closed 4 years ago
2
WIP: Merge some of CRAMFileBAIIndexTest/CRAMFileCRAIIndexTest into a new CRAMFileIndexTest

#1338 jmthibault79 closed 4 years ago
2
The test output is too noisy since we added scala tests.

#1337 yfarjoun opened 5 years ago
0
Call vcfreader.query in in parallel having strange unpredicted behaviors.

#1336 wavefancy closed 5 years ago
1
invalid uncompressedLength

#1335 wavefancy closed 5 years ago
2
SortingCollection logging should only be if DEBUG

#1334 alecw closed 5 years ago
3
BROKEN: use ReferenceContext for CRAMContainerScreenWriter refSeqIndex

#1333 jmthibault79 closed 5 years ago
1
Use ReferenceContext for CramCompressionRecord sequenceId and mateSequenceID

#1332 jmthibault79 closed 5 years ago
2
Spotbugs remaining fixes

#1331 lbergelson closed 5 years ago
2
Spotbugs fix tests

#1330 lbergelson closed 5 years ago
2
Follow-up to #1276: Remove multiple versions of Slice/Container getCRAIEntries()

#1329 jmthibault79 closed 5 years ago
1
Make VariantContextWriterBuilder warn when indexing-on-the-fly is enabled for stream output

#1328 jamesemery closed 5 years ago
2
Yf add interval list codec

#1327 yfarjoun closed 5 years ago
4
Test ContainerIO.calculateSliceOffsetsAndSizes() and fix the slice size calculation

#1326 jmthibault79 closed 5 years ago
1
Fix signing task in build.gradle

#1325 lbergelson closed 5 years ago
1
Reject BCF files when minor version doesn't match the current implementation.

#1324 cmnbroad closed 5 years ago
1
BCF version detection is too permissive

#1323 cmnbroad closed 5 years ago
0
Fixed issue #1111 in broadinstitute/picard

#1322 Sonik-zirael closed 5 years ago
3
Adding back a removed method

#1321 lbergelson closed 5 years ago
3
Adding tests revealing 0-length interval nonsense

#1320 lbergelson opened 5 years ago
0
CRAM: correct CT and MF encoding datatypes from byte to int

#1319 jmthibault79 closed 5 years ago
1
Fixing zero-length interval bug in IntervalList.merge

#1318 lbergelson closed 5 years ago
5
Revert singletonList optimization in SamRecordSetBuilder

#1317 lbergelson closed 5 years ago
2
Changing to use SingletonList in Sam

#1316 lbergelson closed 5 years ago
0
Deprecate TestUtil.deleteRecursively

#1315 lbergelson closed 5 years ago
1
Fix CSI bug when querying files with long references.

#1314 lbergelson closed 5 years ago
3
Deprecate redundant method deleteRecursively in TestUtils

#1313 lbergelson closed 5 years ago
2
CRAM: some structure test cleanup

#1312 jmthibault79 closed 5 years ago
2
Fix bug when loading indexed bgzip fasta file.

#1311 lbergelson closed 5 years ago
2

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