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Issues list

Suggestion on effective VCF file reading?
#305 by dotinspace was closed Apr 10, 2024
2
dict command after cljam 0.8.2 fails bug
#295 by totakke was closed May 13, 2024
2
@alumi
4
Replacing LSB protocol
#289 by athos was closed Dec 13, 2023
3 tasks done
@athos
1
Coding style fixes from clj-kondo's linter with default :off
#273 by niyarin was closed Dec 13, 2023
@niyarin
Features for validating VCF/SAM records enhancement
#271 by athos was closed Dec 13, 2023
@niyarin
2
Case insensitive support for NaN/Infinity bug
#270 by athos was closed Jun 9, 2023
1
@niyarin
2
QUAL value overflows when writing VCF
#267 by nuggetoriniku was closed Apr 11, 2023
1
bgzipped VCF file over HTTP causes infinite loop bug
#259 by totakke was closed Apr 14, 2023
4
Bgziped VCF is illegal.
#251 by niyarin was closed Dec 27, 2021
1
3
Problem that it takes a long time to create an index file from VCF / BCF with many columns.
#240 by niyarin was closed Jun 28, 2021
1
Ambiguity in empty SEQ representation of SAM/BAM format bug
#238 by athos was closed Jun 22, 2021
1
@niyarin
The use of ByteBuffer & CharBuffer breaks cljam's binary compatibility bug
#158 by athos was closed Dec 26, 2018
1
Seemingly useless nil entry occasionally included in VCF parsing results bug
#155 by athos was closed Nov 22, 2018
1
@alumi
Random read of 2bit is quite slower than FASTA
#150 by totakke was closed Nov 2, 2018
@alumi
Support CIGARs longer than 65535 operations enhancement
#142 by alumi was closed Dec 13, 2022
1
@matsutomo81
Create an index file while writing a sorted BAM file enhancement
#141 by alumi was closed Jun 18, 2020
@xckitahara
1
Character escaping in VCF string fields
#136 by athos was closed Jul 6, 2018
1
exec binary does not work on Java 9+ bug
#133 by totakke was closed Jun 22, 2018
9
May need to fix a test for bam-reader with :chr argument
#62 by ayamada was closed May 10, 2017
1
Add tests to check generated data correctness
#61 by ayamada was closed Jun 2, 2017
6 of 7 tasks
6
Losing contigs from VCF info
#23 by mladvladimir was closed Feb 21, 2017
3
Removing dupricate reads enhancement
#2 by totakke was closed Mar 18, 2020
@totakke
3
Wrong FASTA index bug
#1 by totakke was closed Apr 12, 2014
@totakke
1
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