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Issues list

Failure getting reference bases inadequately describes the missing index error cram
#1732 opened Dec 3, 2024 by multimeric updated Dec 3, 2024
1
CRAM: 8-Bin Base Quality Compression cram
#1658 opened Mar 8, 2023 by JWollnik updated Mar 14, 2023
1
CRAM files have zero-length blocks with a compression method associated with them (so cannot be decompressed). bug cram
#1633 opened Nov 8, 2022 by jkbonfield updated Nov 18, 2022
1
SAMFileHeader in CRAM files is missing attributes required by the CRAM spec cram
#506 opened Feb 29, 2016 by cmnbroad updated May 9, 2022
1
3
Add support for reserializing CRAM containers cram
#1606 opened Apr 20, 2022 by cmnbroad updated Apr 20, 2022
1
@cmnbroad
Add CRAM compliance tests against hts-specs test files cram
#1587 opened Dec 20, 2021 by cmnbroad updated Dec 20, 2021
CRAM random access very slow cram
#1162 opened Jul 6, 2018 by eugenegardner updated Jun 29, 2020
@cmnbroad
8
CRAM huffman codeword is limited to 32 bits cram
#1465 opened Mar 17, 2020 by cmnbroad updated Mar 17, 2020
CRAM 2.1 test files have incorrect container block byte sizes cram
#1452 opened Jan 17, 2020 by cmnbroad updated Jan 17, 2020
*N cigar op and CRAM slice headers cram
#1088 opened Feb 15, 2018 by jkbonfield updated Oct 27, 2019
1
Inefficient random access patterns cram
#1424 opened Oct 8, 2019 by jkbonfield updated Oct 15, 2019
3
Enforcing CRAM spec compliance (must have nonzero External Content ID) causes test failures cram
#1232 opened Nov 29, 2018 by jmthibault79 updated Jun 26, 2019
4
Factor and rename the CRAM ReferenceSource class cram
#604 opened May 12, 2016 by cmnbroad updated May 14, 2019
1
CRAM Multi-ref slice indexing is inefficient cram
#1347 opened Apr 3, 2019 by cmnbroad updated Apr 3, 2019
2
Figure out there is a bug in BAMIndexMetaData.recordMetaData cram discussion
#401 opened Dec 2, 2015 by lbergelson updated Mar 12, 2019
1
References in different order to headers bug cram
#1271 opened Feb 1, 2019 by jkbonfield updated Mar 6, 2019
8
CRAM: Interaction between APDelta and Multi-Reference Slices cram
#1218 opened Nov 1, 2018 by jmthibault79 updated Mar 5, 2019
@jmthibault79
1
SAM->CRAM->SAM round-tripping doesn't preserve unsigned attributes as unsigned cram
#499 opened Feb 23, 2016 by cmnbroad updated Feb 19, 2019
3
CRAM 2.1 doesn't handle reads with missing bases correctly cram
#509 opened Mar 2, 2016 by cmnbroad updated Feb 19, 2019
2
CRAM: types for HUFFMAN codecs cram
#518 opened Mar 9, 2016 by jkbonfield updated Feb 19, 2019
2
BAMIndexMetaData incorrect when index results from .crai->.bai conversion cram
#531 opened Mar 21, 2016 by cmnbroad updated Feb 19, 2019
4
CRAM bug with ambiguous bases bug cram
#778 opened Jan 5, 2017 by jkbonfield updated Feb 19, 2019
8
Bam->CRAM loses MQ, start, cigar on unmapped reads cram
#714 opened Sep 22, 2016 by cmnbroad updated Feb 19, 2019
7
Bam->CRAM doesn't always preserve cigar elements identically cram
#713 opened Sep 22, 2016 by cmnbroad updated Feb 19, 2019
4
BAM->CRAM conversion doesn't handle supplementary reads correctly cram
#802 opened Feb 10, 2017 by cmnbroad updated Feb 19, 2019
2
ProTip! Updated in the last three days: updated:>2025-01-02.