chrovis/cljam

Issues

• Problematic behaviors around BAM index generation

  #316 opened 5 months ago by athos
  0

• SAM/BAM/CRAM readers don't support @CO header

  #315 opened 5 months ago by athos
  0

• Read/write invariance breaks with integer tags in BAM/CRAM

  #314 opened 5 months ago by athos
  0

• `dict` command after cljam 0.8.2 fails

  #295 opened 6 months ago by totakke
  4

• Suggestion on effective VCF file reading?

  #305 opened 8 months ago by dotinspace
  2

• Test coverage fails sometimes on some environments

  #301 opened 9 months ago by athos
  0

• Coding style fixes from clj-kondo's linter with default :off

  #273 opened a year ago by niyarin
  0

• Features for validating VCF/SAM records

  #271 opened a year ago by athos
  2

• Replacing LSB protocol

  #289 opened a year ago by athos
  1

• CRAM support?

  #223 opened 4 years ago by indraniel
  1

• Case insensitive support for NaN/Infinity

  #270 opened a year ago by athos
  2

• Report position in read for reads in a pileup

  #274 opened a year ago by alumi
  0

• bgzipped VCF file over HTTP causes infinite loop

  #259 opened 2 years ago by totakke
  4

• QUAL value overflows when writing VCF

  #267 opened 2 years ago by nuggetoriniku
  0

• Support CIGARs longer than 65535 operations

  #142 opened 2 years ago by alumi
  0

• Add tests to check generated data correctness

  #61 opened 7 years ago by ayamada
  6

• Bgziped VCF is illegal.

  #251 opened 3 years ago by niyarin
  3

• Problem that it takes a long time to create an index file from VCF / BCF with many columns.

  #240 opened 3 years ago by niyarin
  0

• Ambiguity in empty SEQ representation of SAM/BAM format

  #238 opened 3 years ago by athos
  0

• Create an index file while writing a sorted BAM file

  #141 opened 4 years ago by alumi
  1

• Removing dupricate reads

  #2 opened 5 years ago by totakke
  3

• The use of ByteBuffer & CharBuffer breaks cljam's binary compatibility

  #158 opened 6 years ago by athos
  0

• Seemingly useless nil entry occasionally included in VCF parsing results

  #155 opened 6 years ago by athos
  0

• Random read of 2bit is quite slower than FASTA

  #150 opened 6 years ago by totakke
  0

• `mpileup` loses bases of alignments starting with a insertion

  #139 opened 6 years ago by alumi
  0

• Character escaping in VCF string fields

  #136 opened 6 years ago by athos
  1

• ##META meta info support for VCF/BCF

  #137 opened 6 years ago by athos
  0

• exec binary does not work on Java 9+

  #133 opened 6 years ago by totakke
  9

• May need to fix a test for bam-reader with `:chr` argument

  #62 opened 8 years ago by ayamada
  1

• Losing contigs from VCF info

  #23 opened 8 years ago by mladvladimir
  3

• Pileup reads with adjacent indels.

  #28 opened 8 years ago by alumi
  1

• Wrong FASTA index

  #1 opened 11 years ago by totakke
  1