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Issues list

Failure getting reference bases inadequately describes the missing index error cram
#1732 opened Dec 3, 2024 by multimeric
1
CRAM: 8-Bin Base Quality Compression cram
#1658 opened Mar 8, 2023 by JWollnik
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
1
Add support for reserializing CRAM containers cram
#1606 opened Apr 20, 2022 by cmnbroad
1
@cmnbroad
Add CRAM compliance tests against hts-specs test files cram
#1587 opened Dec 20, 2021 by cmnbroad
CRAM huffman codeword is limited to 32 bits cram
#1465 opened Mar 17, 2020 by cmnbroad
CRAM 2.1 test files have incorrect container block byte sizes cram
#1452 opened Jan 17, 2020 by cmnbroad
Inefficient random access patterns cram
#1424 opened Oct 8, 2019 by jkbonfield
3
CRAM Multi-ref slice indexing is inefficient cram
#1347 opened Apr 3, 2019 by cmnbroad
2
References in different order to headers bug cram
#1271 opened Feb 1, 2019 by jkbonfield
8
CRAM should validate the SAM header against the reference being used cram
#1244 opened Dec 19, 2018 by cmnbroad
CRAM: better testing of unmapped reads cram
#1236 opened Dec 4, 2018 by jmthibault79
Enforcing CRAM spec compliance (must have nonzero External Content ID) causes test failures cram
#1232 opened Nov 29, 2018 by jmthibault79
4
CRAM: Interaction between APDelta and Multi-Reference Slices cram
#1218 opened Nov 1, 2018 by jmthibault79
@jmthibault79
1
CramComplianceTest: four tests from htslib fail due to SAMRecord mismatch cram
#1189 opened Oct 5, 2018 by jmthibault79
CRAM random access very slow cram
#1162 opened Jul 6, 2018 by eugenegardner
@cmnbroad
8
CRAM NPE when writing using an unindexed fasta reference cram
#1152 opened Jun 19, 2018 by lbergelson
Closure of OutputStream in class CRAMContainerStreamWriter cram
#1092 opened Feb 20, 2018 by fversaci
*N cigar op and CRAM slice headers cram
#1088 opened Feb 15, 2018 by jkbonfield
1
CRAM header (and thus md5) varies depending on location of the file when it was created. cram
#1068 opened Jan 11, 2018 by cmnbroad
1
Reading a CRAM using a reference file with no dictionary gives misleading error message bug cram
#998 opened Sep 26, 2017 by cmnbroad
Error executing two sequential SamReader.queryOverlapping() calls for a CRAM File bug cram
#918 opened Jun 26, 2017 by skashin
1
Make CRAMFileReader works with CRAI directly cram
#851 opened Apr 11, 2017 by kamyshova
BAM->CRAM conversion doesn't handle supplementary reads correctly cram
#802 opened Feb 10, 2017 by cmnbroad
2
CRAM bug with ambiguous bases bug cram
#778 opened Jan 5, 2017 by jkbonfield
8
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