mozack/abra

Issues

• java.lang.IllegalStateException

  #46 opened 2 years ago by lovelycatZ
  0

• build issue

  #45 opened 3 years ago by BJWiley233
  0

• abra2 error java.lang.NumberFormatException

  #44 opened 5 years ago by rimzaag
  3

• No contigs assembled: no space left on device

  #43 opened 6 years ago by toddcreasy
  1

• Abra will realign duplicates?

  #39 opened 6 years ago by ionox0
  5

• Is it possible to get the assembled contig?

  #42 opened 6 years ago by juberpatel
  2

• Abra processes unique reads?

  #41 opened 6 years ago by ionox0
  2

• Testing practices

  #40 opened 6 years ago by ionox0
  2

• Is YA tag deterministic?

  #38 opened 6 years ago by ionox0
  4

• Change header in bam

  #37 opened 6 years ago by FedikZe
  1

• Abra error

  #36 opened 7 years ago by yuhongning
  2

• hidden dependency on bwa mem

  #34 opened 7 years ago by covingto
  2

• xlC compatibility - C++ STL referenced in .c files

  #32 opened 7 years ago by jlost
  4

• Amplicon data

  #31 opened 8 years ago by mcgml
  5

• [Request] Replace System.out.print* statements with System.err.print* for stream compatibility

  #29 opened 8 years ago by dnbaker
  3

• Error in Cadabra

  #28 opened 8 years ago by GKerdivel
  4

• Exception in thread Error

  #26 opened 8 years ago by tinuthomas
  2

• polyA/polyT/lowcomplexity region realignments for single ended reads

  #25 opened 8 years ago by avilella
  3

• [fwrite] Remote I/O error

  #24 opened 9 years ago by bcantarel
  5

• Excessive run time

  #23 opened 9 years ago by dh10
  2

• Bug in BED file parsing

  #22 opened 9 years ago by marc-sturm
  0

• Error running abra [0.96]

  #21 opened 9 years ago by chisqr
  4

• Trouble with GATK due to Cigar representation

  #10 opened 9 years ago by joonlee3
  2

• Requested array size exceeds VM limit

  #11 opened 9 years ago by joonlee3
  4

• java.lang.UnsatisfiedLinkError

  #16 opened 9 years ago by preciserobot
  2

• New java.lang.ArrayIndexOutOfBoundsException: 44800 Issue

  #17 opened 9 years ago by mgfield
  1

• Running ABRA on BAM files generated from the GATK pepeline

  #19 opened 9 years ago by chisqr
  1

• Error while running ABRA

  #20 opened 9 years ago by chisqr
  6

• Errors without BED file

  #18 opened 9 years ago by adammaikai
  1

• java.lang.NegativeArraySizeException

  #12 opened 9 years ago by etwatson
  9

• Problem finding bwa index when running ABRA

  #14 opened 9 years ago by mgfield
  3

• Error running on customs bed file

  #15 opened 9 years ago by rhshah
  10

• does abra realign unaligned reads

  #13 opened 10 years ago by dwaggott
  6

• 'align_to_contig.sam.sai' : No such file or directory

  #7 opened 10 years ago by dh10
  3

• License?

  #2 opened 10 years ago by tdanford
  4

• somatic mode

  #9 opened 10 years ago by joonlee3
  1

• Weird error ...

  #8 opened 10 years ago by joonlee3
  4

• Exception in thread "Thread-212177" java.lang.OutOfMemoryError: PermGen space

  #6 opened 10 years ago by Gig77
  4

• Bug in v0.77 - Input regions not split properly

  #4 opened 10 years ago by mozack
  0

• Read name length exceeded

  #3 opened 10 years ago by Gig77
  2

• BWA error: fail to locate the index files

  #5 opened 10 years ago by Gig77
  5

• SAM Read name length exceeded

  #1 opened 11 years ago by jstjohn
  1