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samtools
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htsjdk
A Java API for high-throughput sequencing data (HTS) formats.
http://samtools.github.io/htsjdk/
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Add support for re-serializing (sharding and reassembling) CRAM containers.
#1609
cmnbroad
opened
2 years ago
1
Would it be OK to remove the Travis app from the Samtools organisation?
#1608
daviesrob
closed
2 years ago
3
Make the CRAM MD5 failure message more user friendly.
#1607
cmnbroad
closed
2 years ago
0
Add support for reserializing CRAM containers
#1606
cmnbroad
opened
2 years ago
0
Support CRAM reference regions.
#1605
cmnbroad
closed
2 years ago
2
Question: Gettting SAMFileHeader from partial files or byte chunks.
#1604
gariem
closed
1 year ago
3
Remove validateArg call with a high invocation count when writing CRAM.
#1603
cmnbroad
closed
11 months ago
2
Remove unncessary println.
#1602
cmnbroad
closed
2 years ago
1
Change queryname sort to match samtools
#1601
nh13
opened
2 years ago
1
Implementation of a SAMRecord comparator that matches samtools' queryname sort order.
#1600
tfenne
opened
2 years ago
9
Add an option to SAMFileWriter to disable checking of ordering or rec…
#1599
tfenne
closed
2 years ago
6
Give VCFEncoder an option to print float values with full precision
#1598
roland-ewald
opened
2 years ago
0
Support IGV "browse mode" CRAM decoding
#1597
cmnbroad
closed
2 years ago
2
VCF 4.3 writing.
#1596
cmnbroad
opened
2 years ago
1
Support loading of CSI from URLs/streams.
#1595
cmnbroad
closed
2 years ago
2
Update to a version of snappy that natively supports apple silicon.
#1594
tfenne
closed
2 years ago
3
Use allele info in VariantContext comparisons for stable sorts
#1593
clintval
closed
1 year ago
7
Fix decoding of CRAM Scores read feature during normalization.
#1592
cmnbroad
closed
2 years ago
0
SamReader's close method doesn't seem to work
#1591
wangyuxiang985
opened
2 years ago
0
Fix restoration of read base feature code.
#1590
cmnbroad
closed
2 years ago
2
htsget requests are not following redirects?
#1589
jrobinso
closed
1 year ago
3
Add VCF compliance tests against hts-specs test files
#1588
cmnbroad
opened
2 years ago
0
Add CRAM compliance tests against hts-specs test files
#1587
cmnbroad
opened
2 years ago
0
Can HTSJDK use a VCF index to quickly count total records in a VCF?
#1586
bbimber
opened
2 years ago
9
Update explain samflags script to python3
#1585
lbergelson
closed
2 years ago
2
Unmapped read validation causes validation errors in specifications-compliant records.
#1584
d-cameron
opened
2 years ago
3
Upgrade to samtools 1.14.
#1583
cmnbroad
closed
2 years ago
1
Switching to Python3
#1582
pgrt
closed
2 years ago
1
VCFHeader and VCFHeaderLine rewrite/refactoring
#1581
cmnbroad
opened
2 years ago
6
Update to new version of the snappy compatible with M1 macs
#1580
lbergelson
closed
2 years ago
1
Add CRAM validation tests against the test files in the hts-specs repo
#1579
cmnbroad
closed
2 years ago
1
ignore TC, TN on CRAM read
#1578
yash-puligundla
closed
2 years ago
7
Introduce non-throwing version validation methods for VCFHeaderLine
#1577
andersleung
closed
2 years ago
0
Rename ByteArrayAlelle to SimpleAllele and make it public
#1576
lbergelson
closed
2 years ago
1
add predicate to GFF3Codec to give a chance to filter out some unused attributes
#1575
lindenb
closed
2 years ago
2
Merging VCFHeaders can result in incorrectly ordered contig lines
#1574
cmnbroad
opened
2 years ago
0
VCFHeader shouldn't allow multiple VCFContigHeaderLines with the same contig index
#1573
cmnbroad
opened
2 years ago
0
Adding Github actions as an alternative to travis.
#1572
lbergelson
closed
2 years ago
2
Don't write obsolete data series TC and TN to CRAM
#1571
cmnbroad
closed
2 years ago
1
Add flag to open CRAM file without reference sequence
#1570
jdotsoft
closed
2 years ago
3
handle utf-8 encoding
#1569
yash-puligundla
opened
3 years ago
3
remove hardcoded .idx
#1568
yash-puligundla
closed
3 years ago
1
add file format to index is required error message
#1567
yash-puligundla
closed
3 years ago
2
Add context to exception when the .vcf file is invalid
#1566
yash-puligundla
closed
3 years ago
2
Unclear what the exception is referring to when htsjdk is used to validate a NIST .vcf file
#1565
namra1
closed
3 years ago
3
Some long reads tests using PacBio data.
#1564
cmnbroad
closed
3 years ago
1
Allow chaining setters for SAMSequenceRecord
#1563
rickymagner
closed
2 years ago
1
Setters should return `this` for chaining
#1562
rickymagner
closed
2 years ago
1
Validate that SAM header tag keys are exactly 2 characters long
#1561
jmarshall
closed
3 years ago
1
CG tag has the incorrect type.
#1560
jkbonfield
opened
3 years ago
1
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