mozack/abra2

Issues

• abra2 error java.lang.NumberFormatException

  #25 opened 5 years ago by rimzaag
  4

• Abra2-processed bams are incompatible with Strelka2

  #61 opened 3 months ago by lculibrk
  0

• v2.24 gives "Error loading: libAbra.so", older versions do not

  #46 opened 3 years ago by chrisamiller
  7

• Specific case that ABRA2 is not realigning correctly

  #60 opened 5 months ago by parsaeskandar
  0

• How to shorten run time

  #58 opened 9 months ago by jingjing578
  4

• IndelRealigner-parameters vs Abra2-parameters

  #59 opened 8 months ago by Manuel-DominguezCBG
  1

• build fails on linux

  #57 opened 10 months ago by yangxingyu588
  0

• Unknown format conversion exception

  #56 opened 10 months ago by abhiku0007
  0

• Fusions

  #55 opened a year ago by gitMakeCoffee
  0

• Abra2 creating large (around 100bp) deletions to alignment

  #54 opened a year ago by rchapman2000
  0

• java.lang.OutOfMemoryError: Java heap space

  #52 opened 2 years ago by AdilyAid
  1

• Abra and log4j

  #51 opened 3 years ago by colindaven
  0

• Alternate or duplicate alignment in output

  #50 opened 3 years ago by jgaupp-invitae
  1

• java.lang.IllegalArgumentException: Invalid reference index -1

  #48 opened 3 years ago by ThanosPAS
  1

• Score threshold and content of the printed INFO

  #49 opened 3 years ago by camillebenoist
  0

• max_paths_from_root

  #45 opened 3 years ago by warthmann
  3

• Option to prevent reads ending with complex indel

  #24 opened 5 years ago by jakobmatthes
  7

• Num reads to scan for read length/insert length/mapq

  #44 opened 3 years ago by danoreper
  0

• java.lang.IllegalArgumentException: Contig too long

  #39 opened 4 years ago by warthmann
  4

• Bed file format

  #43 opened 4 years ago by V-Catherine
  1

• workflow of data pre-processing of RNAseq

  #41 opened 4 years ago by SaHash
  6

• Expected memory requirements

  #33 opened 5 years ago by ionox0
  7

• feature request: stdin functionality

  #42 opened 4 years ago by eboyden
  0

• Realigned output bam TLEN field plus/minus sign when FLAG == 147

  #40 opened 4 years ago by Julie-Zhongyun-Huang
  2

• crash with java IndexOutOfBoundsException

  #18 opened 6 years ago by anso-sertier
  26

• YO tag format

  #32 opened 5 years ago by ionox0
  6

• MD tags for realigned reads

  #31 opened 5 years ago by rawagiha
  4

• Identical runs give slightly different results

  #36 opened 5 years ago by sfrenk
  8

• Compilation on Mac

  #38 opened 5 years ago by edgardomortiz
  0

• compilation terminated during make

  #37 opened 5 years ago by zhoutengsheng
  3

• glibc2.14

  #35 opened 5 years ago by Tjitskedv
  2

• Abra2 output BAM processing

  #34 opened 5 years ago by roysomak4
  2

• Supplementary alignment behavior question

  #29 opened 5 years ago by dstreett
  1

• what's wrong with that ref

  #27 opened 5 years ago by panxiaoguang
  1

• abra2 break the order of sam file tags.

  #26 opened 5 years ago by y9c
  1

• Invalid read written

  #22 opened 6 years ago by marc-sturm
  1

• Using abra/abra2 for local assembly of pacbio reads?

  #20 opened 6 years ago by ggstatgen
  1

• Increase MAX_SAMPLES to 12 or 16

  #21 opened 6 years ago by ckandoth
  2

• Comparison with GATK's IndelRealigner?

  #17 opened 6 years ago by iskandr
  4

• Crash when target region BED file contains header lines

  #16 opened 7 years ago
  3

• IndexOutOfBoundsException at AltContigGenerator.java#L273

  #14 opened 7 years ago by hemp
  2

• Explosion on CIGARS using = and X operators

  #15 opened 7 years ago by Lenbok
  3

• the software is great ,but i still has a problom,it will leave some reads un-gapped,like the figure show,i want known why those reads un-gapped? if those reads gapped,they all are perfect match the del,and have no mismatches.

  #8 opened 7 years ago by 522845911
  1

• Generating BED targets

  #12 opened 7 years ago by Asutu
  2

• UnsatisfiedLinkError on Mac OS

  #13 opened 7 years ago by Asutu
  2

• ABRA versions starting from v2.07 crash with single end data

  #10 opened 7 years ago by mfoll
  2

• crash with java IndexOutOfBoundsException

  #7 opened 7 years ago by wongs2
  11

• Negative Array Size Exception

  #9 opened 7 years ago by drsuuzzz
  7

• Nog4j2 error message.

  #6 opened 7 years ago by wongs2
  1

• abra 2.07 removes half of pair completely

  #5 opened 7 years ago by lordzappo
  5