statgen/bamUtil

Issues

• Erroneous CIGAR string after clipOverlap

  #72 opened 8 months ago by MboiTui
  2

• Do not use makefiles from libStatGen

  #73 opened 4 months ago by alexreg
  0

• `bam diff` seems to return the reads that look identical between A and B

  #59 opened 5 years ago by hisplan
  1

• splitChromosome without header?

  #71 opened 9 months ago by jtmorgan0
  0

• License?

  #70 opened a year ago by jjv5
  1

• Odd stats reported for clipOverlap

  #69 opened 2 years ago by joegeorgeson
  0

• build is broken due to deprecated git protocol

  #67 opened 3 years ago by ahvigil
  1

• bamutil diff - Get record for every read being compared

  #66 opened 3 years ago by DavidStreid
  2

• can not install with conda

  #65 opened 3 years ago by Frank1219
  2

• bash -x testBam2FastQ.sh and bash -x testMergeBam.sh failed on centos8_aarch64

  #64 opened 3 years ago by Tom-python0121
  0

• bam2FastQ generates empty fastq files

  #63 opened 3 years ago by LanyingMa
  0

• BamUtil: recab error: failed to open reference genome

  #62 opened 4 years ago by cbostwick87
  6

• Error building from source: libStatGen

  #61 opened 4 years ago by moldach
  3

• the clang compiler does not support -pg option on versions of OS X 10.9 and later

  #60 opened 5 years ago by TommySchooner
  4

• `bam diff` should exit with a return code

  #54 opened 6 years ago by hisplan
  0

• Makefile should not ignore system LDFLAGS

  #58 opened 5 years ago by bichkd
  0

• cannot consume -.ubam on a pipe

  #57 opened 5 years ago by bwlang
  2

• Compilation doesn't work (warnings=errors)

  #45 opened 7 years ago by Tsallagov
  5

• Cannot Compile NonPrimaryDedup Branch

  #56 opened 5 years ago by BrenKenna
  5

• The output of make Clonelib should be clearer

  #19 opened 9 years ago by pjvandehaar
  3

• Dedup does not work from std/in

  #55 opened 6 years ago by slazicoicr
  2

• No output

  #14 opened 9 years ago by AmirKamali
  3

• Cut middle of reads

  #53 opened 6 years ago by shimbalama
  2

• Building bamUtil returns error: undefined reference

  #52 opened 6 years ago by Dlfn
  4

• clipoverlap on raw output straight from bwa

  #51 opened 6 years ago by bjkelly
  3

• Compile error

  #50 opened 7 years ago by LiyanJi-code
  4

• Building bamUtil returns error: call of overloaded 'to_string(int&)' is ambiguous

  #49 opened 7 years ago by sam0per
  4

• clipOverlap in outward facing pairs

  #48 opened 7 years ago by dariober
  1

• bam diff when 2 reads have indentical names AND start positions?

  #47 opened 7 years ago by anderspitman
  1

• How to cite bamUtil

  #46 opened 7 years ago by heewookl
  1

• Option to output bamUtil stats to STDOUT rather than to a file

  #44 opened 7 years ago by dylkot
  2

• 1.0.13 labeled as the "latest release" under releases

  #43 opened 8 years ago by heewookl
  1

• Assumption made in code masked by earlier check.

  #42 opened 8 years ago by innovate-invent
  6

• Compiling issue

  #18 opened 9 years ago by kbaySA
  6

• bam2FastQ: fixing output file name whith --gzip

  #28 opened 9 years ago by fgvieira
  1

• Update wiki build insturctions

  #23 opened 9 years ago by andrewrech
  1

• bam recab: parallel processing

  #21 opened 9 years ago by andreas-wilm
  4

• Strelka output using Clipped bams not the same as unclipped bams

  #20 opened 9 years ago
  15

• Indexing the clipped bam files

  #16 opened 9 years ago
  14

• ‘DATE’ / 'USER' was not declared in this scope

  #12 opened 9 years ago by luis-ortiz
  1

• CIGAR does not evaluate to the same length as SEQ

  #17 opened 9 years ago by h-2
  3

• Failed to open bam fille

  #15 opened 9 years ago
  16

• Generating interleaved FASTQ for bam2FastQ?

  #10 opened 10 years ago by alexlancaster
  5

• make error

  #11 opened 11 years ago by songsy
  1

• bam dedup --in /dev/stdin --out /dev/stdout does not work.

  #5 opened 11 years ago by vinjana
  1

• Compilation problems on Linux

  #4 opened 11 years ago by vinjana
  8

• compare reads ignoring read id

  #8 opened 12 years ago by avilella
  1

• new mapqual diff option

  #9 opened 12 years ago by avilella
  1

• bamutil diff speed ups?

  #7 opened 12 years ago by avilella
  1

• Make Error with CentOS

  #6 opened 12 years ago by chaelir
  2