issues
search
samtools
/
htsjdk
A Java API for high-throughput sequencing data (HTS) formats.
http://samtools.github.io/htsjdk/
283
stars
242
forks
source link
issues
Newest
Newest
Most commented
Recently updated
Oldest
Least commented
Least recently updated
Updated the max isize to be Integer.MAX_VALUE.
#1410
tfenne
closed
5 years ago
7
Suppress all exceptions during DeleteOnExitPathHook
#1409
lbergelson
closed
5 years ago
2
Make AbstractFastaSequenceFile serializable by Kryo for Spark.
#1408
tomwhite
closed
5 years ago
3
Quick Question: Can we read a CRAM Header without reference ?
#1407
lindenb
closed
5 years ago
2
- Added option to log with suppliers
#1406
yfarjoun
closed
5 years ago
1
Problem with tribble "has index" logic
#1405
jrobinso
opened
5 years ago
7
NPE introduced in 2.20.0
#1404
lbergelson
closed
5 years ago
0
fix small bug in VariantContextBuilder
#1403
yfarjoun
closed
5 years ago
2
IntervalList not sorted?
#1402
al-dunstan
opened
5 years ago
2
Handle PEDIGREE header lines differently for vcf4.2 vs vcf4.3.
#1401
cmnbroad
closed
5 years ago
2
VCF4.2 PEDIGREE header parsing broken
#1400
brainstorm
closed
5 years ago
2
potential bug in SeekablePathStream.read()
#1399
lbergelson
opened
5 years ago
1
Flaw in tribble tabix test
#1398
jrobinso
closed
5 years ago
6
Optimize AbstractBAMFileIndex#query with test
#1397
lbergelson
closed
5 years ago
3
Optimize AbstractBAMFileIndex#query to avoid quadratic behavior when …
#1396
tomwhite
closed
5 years ago
4
Make Validation error emit the validation type that was violated
#1395
yfarjoun
closed
5 years ago
1
CRAM implementation should reject unrecognized CRAM versions
#1394
cmnbroad
closed
4 years ago
2
Updating issue and PR templates
#1393
lbergelson
closed
5 years ago
1
Describing what our version number means
#1392
lbergelson
closed
5 years ago
0
adding readme section about style guides
#1391
lbergelson
closed
5 years ago
1
Adding a code of conduct document for htsjdk.
#1390
lbergelson
closed
5 years ago
1
Output missing vcf fields as a single .
#1389
lbergelson
closed
5 years ago
1
SamReaderFactory doesn't buffer the index SeekablePathStream
#1388
lbergelson
opened
5 years ago
0
Proposal to change maintainers
#1387
yfarjoun
opened
5 years ago
5
add style guide for IDE's
#1386
mitochon
closed
5 years ago
7
Partially missing AD and PL are treated as empty
#1385
lbergelson
opened
5 years ago
5
Prevent integer overflow in Interval countBases method.
#1384
cmnbroad
closed
5 years ago
3
Handle "nan" in Float attribute regardless of case.
#1383
alecw
closed
5 years ago
1
There should be a constants class for file extensions
#1382
jb-adams
closed
5 years ago
12
update readme with info about reading vcf 4.3
#1381
lbergelson
closed
5 years ago
1
Long reference sequences
#1380
SergejN
opened
5 years ago
0
Bases in 'Bases' read features ('BB' data series) aren't correctly restored on read
#1379
cmnbroad
closed
2 years ago
2
Adding a few more semi-colons in shell in travis config.
#1378
tfenne
closed
5 years ago
0
Read no_ref crams
#1377
JoeRayn
closed
5 years ago
5
Fix to ensure we only publish snapshots compiled with openjdk-8.
#1376
tfenne
closed
5 years ago
3
reverseComplement of SAMRecord does not inverse CigarString
#1375
RobinVanSchendel
closed
5 years ago
4
Substitution matrix refactoring and tests
#1374
cmnbroad
closed
5 years ago
5
Trying to replace SAMFileReader in FastQC: htsjdk.samtools.util.RuntimeIOException: java.io.IOException: Stream closed
#1373
daissi
closed
5 years ago
2
VCF codec should handle multiple missing GL fields
#1372
mitochon
closed
5 years ago
15
GL field handling inconsistent between encoder and decoder
#1371
mitochon
closed
2 years ago
3
Addresses part of issue #18, Allele class refactoring.
#1370
vruano
opened
5 years ago
3
add documention for VariantContext.getStart() regarding telomeric events
#1369
SHuang-Broad
closed
5 years ago
6
get filter null
#1368
YdlNAU
opened
5 years ago
4
CRAM gzip compression doesn't honor samjdk.compression_level
#1367
cmnbroad
closed
4 years ago
2
SubstitutionMatrix class cleanup - part 1.
#1366
cmnbroad
closed
5 years ago
1
VariantContextBuilder : putAttributes fails if Map cannot be modified
#1365
lindenb
closed
5 years ago
1
Tolerate lower-case nans in QUAL
#1364
karenfeng
closed
5 years ago
7
Add support for the TP (topology) tag in the sequence dictionary
#1363
nh13
opened
5 years ago
5
Moved loading of sequence dictionary into a separate, overriddeable me…
#1362
tfenne
closed
5 years ago
5
Change SAMTextHeaderCodec to no longer accumulate the entire text of …
#1361
tfenne
closed
5 years ago
6
Previous
Next