samtools/htsjdk

Issues

• Truncation issue with GZIPInputStream when reading bgzip-compressed streams

  #1691 opened a year ago by jkmatila
  2

• htsjdk.samtools.util.IOUtil.assertFileIsWritable on certain NFS environments fails to correctly assess permissions

  #1671 opened a year ago by jd-daniels
  4

• Incomplete license metadata in build.gradle

  #1710 opened 7 months ago by tapdiego-amzn
  0

• Iterator not working on vcffileReader

  #1701 opened a year ago by AlessandroBalestrucci
  3

• Ambiguous assertions in the tests

  #1695 opened a year ago by pgrt
  1

• Resolve issues around integrating HTTP NIO provider

  #1689 opened a year ago by lbergelson
  0

• Question: Gettting SAMFileHeader from partial files or byte chunks.

  #1604 opened a year ago by gariem
  3

• VariantContext has inconsistent behavior on getting allele type with spanning deletions

  #1686 opened a year ago by rickymagner
  0

• support for Azure blob storage? (specifically access to BAM/CRAM files in Azure blob storage by IGV)

  #1685 opened a year ago by smrgit
  0

• htsget requests are not following redirects?

  #1589 opened a year ago by jrobinso
  3

• IOUtil.openFileForMd5CalculatingWriting() puts the md5 file in the wrong place.

  #1682 opened a year ago by lbergelson
  0

• Add a better error message when the reference is too long for indexing

  #1651 opened 2 years ago by lbergelson
  5

• Deleted Java developers team

  #1673 opened a year ago by lbergelson
  0

• SAMFileWriterFactory creates .bai file when writing .cram file

  #1672 opened a year ago by rickymagner
  1

• Error when reading a VCF 4.3 file with spaces in INFO field values

  #1667 opened 2 years ago by jkmatila
  1

• SamReaderFactory should use current defaults when makeDefault() is called

  #1666 opened 2 years ago by lbergelson
  0

• Question: How to generate FAI files and TBI files

  #1665 opened 2 years ago by Lys9527
  5

• Question: how to code a GTFCodec beside of the existing GFF3Codec

  #1613 opened 2 years ago by lindenb
  1

• CRAM: 8-Bin Base Quality Compression

  #1658 opened 2 years ago by JWollnik
  1

• Escaped doublequotes in INFO descriptions result in invalid VCF file

  #1661 opened 2 years ago by bartcharbon
  2

• SamReader slower than expected on network drive

  #1660 opened 2 years ago by BeatWolf
  1

• Histogram class uses unsafe methods for returning min/max

  #1657 opened 2 years ago by rickymagner
  0

• Unmapped read validation causes validation errors in specifications-compliant records.

  #1584 opened 3 years ago by d-cameron
  3

• Question: Tabix index to find min(POS) and max(POS) in each contig

  #1652 opened 2 years ago by lindenb
  0

• Race conditions accessing CRAM's reference data through ReferenceSource

  #1643 opened 2 years ago by vruano
  0

• VCF sorting change breaks existing VCFs

  #1637 opened 2 years ago by lbergelson
  1

• CRAM files have zero-length blocks with a compression method associated with them (so cannot be decompressed).

  #1633 opened 2 years ago by jkbonfield
  1

• LittleEndianInputStream EOF test is incorrect

  #1614 opened 3 years ago by cmnbroad
  9

• Our FastaSequenceIndex too large to fit in memory

  #1630 opened 2 years ago by wbazant
  4

• The last-but-one argument of test testQueryAlignmentStart in HtsCRAMCodec30And21QueryTest.java is long

  #1631 opened 2 years ago by pgrt
  1

• Nashorn engine removed from OpenJDK 17 causes htsjdk to throw exceptions

  #1611 opened 2 years ago by pgrt
  2

• What is the non-deprecated replacement for acceptableAlleleBases?

  #1623 opened 2 years ago by danking
  4

• Switching to Python3

  #1582 opened 2 years ago by pgrt
  1

• Would it be OK to remove the Travis app from the Samtools organisation?

  #1608 opened 2 years ago by daviesrob
  3

• EdgeReadIterator (used in Picard's CollectWgsMetrics) doesn't handle intervals correctly

  #1615 opened 2 years ago by michaelgatzen
  2

• IntervalTree.Node's methods have package visibility only

  #1620 opened 2 years ago by holtgrewe
  1

• Support IGV "browse mode" CRAM decoding

  #1597 opened 3 years ago by cmnbroad
  2

• Remove validation of VCF Header line field order?

  #1610 opened 3 years ago by tfenne
  1

• Add flag to open CRAM file without reference sequence

  #1570 opened 3 years ago by jdotsoft
  3

• Add support for reserializing CRAM containers

  #1606 opened 3 years ago by cmnbroad
  0

• Give VCFEncoder an option to print float values with full precision

  #1598 opened 3 years ago by roland-ewald
  0

• SamReader's close method doesn't seem to work

  #1591 opened 3 years ago by wangyuxiang985
  0

• Add CRAM validation tests against the test files in the hts-specs repo

  #1579 opened 3 years ago by cmnbroad
  1

• Don't write obsolete data series TC and TN to CRAM

  #1571 opened 3 years ago by cmnbroad
  1

• Add VCF compliance tests against hts-specs test files

  #1588 opened 3 years ago by cmnbroad
  0

• Add CRAM compliance tests against hts-specs test files

  #1587 opened 3 years ago by cmnbroad
  0

• Can HTSJDK use a VCF index to quickly count total records in a VCF?

  #1586 opened 3 years ago by bbimber
  9

• VCFHeader shouldn't allow multiple VCFContigHeaderLines with the same contig index

  #1573 opened 3 years ago by cmnbroad
  0

• Merging VCFHeaders can result in incorrectly ordered contig lines

  #1574 opened 3 years ago by cmnbroad
  0

• Unclear what the exception is referring to when htsjdk is used to validate a NIST .vcf file

  #1565 opened 3 years ago by namra1
  3