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Issues list

Possible issues for large genome (No index is available for this BAM file. and exceeding integer length in GTF file)
#64 opened Jan 17, 2025 by JuiTse
abra2 error java.lang.NumberFormatException
#63 opened Dec 4, 2024 by C-YONG
Window size vs targets - using targets only?
#62 opened Nov 20, 2024 by ranasats
3
Abra2-processed bams are incompatible with Strelka2
#61 opened Apr 10, 2024 by lculibrk
Specific case that ABRA2 is not realigning correctly
#60 opened Feb 12, 2024 by parsaeskandar
IndelRealigner-parameters vs Abra2-parameters
#59 opened Nov 9, 2023 by Manuel-DominguezCBG
1
How to shorten run time
#58 opened Oct 13, 2023 by jingjing578
4
build fails on linux
#57 opened Sep 9, 2023 by yangxingyu588
Unknown format conversion exception
#56 opened Aug 26, 2023 by abhiku0007
1
Fusions
#55 opened Mar 24, 2023 by gitMakeCoffee
Abra2 creating large (around 100bp) deletions to alignment
#54 opened Mar 6, 2023 by rchapman2000
java.lang.OutOfMemoryError: Java heap space
#52 opened Sep 11, 2022 by AdilyAid
1
Abra and log4j
#51 opened Dec 14, 2021 by colindaven
Score threshold and content of the printed INFO
#49 opened Nov 12, 2021 by camillebenoist
java.lang.IllegalArgumentException: Invalid reference index -1
#48 opened Oct 14, 2021 by ThanosPAS
1
v2.24 gives "Error loading: libAbra.so", older versions do not
#46 opened Sep 15, 2021 by chrisamiller
7
max_paths_from_root
#45 opened Aug 23, 2021 by warthmann
3
Num reads to scan for read length/insert length/mapq
#44 opened Jun 7, 2021 by danoreper
Bed file format
#43 opened Jun 18, 2020 by V-Catherine
1
feature request: stdin functionality
#42 opened Feb 29, 2020 by eboyden
Realigned output bam TLEN field plus/minus sign when FLAG == 147
#40 opened Jan 16, 2020 by Julie-Zhongyun-Huang
2
Compilation on Mac
#38 opened Aug 15, 2019 by edgardomortiz
compilation terminated during make
#37 opened Jul 21, 2019 by zhoutengsheng
3
Expected memory requirements
#33 opened May 1, 2019 by ionox0
7
Supplementary alignment behavior question
#29 opened Mar 12, 2019 by dstreett
1
ProTip! What’s not been updated in a month: updated:<2025-01-07.