COMBINE-lab/pufferfish

Issues

• Fails to compile on IBM Power architecture (ppc64le)

  #47 opened a year ago by jblachly
  0

• can't install pufferfish

  #46 opened a year ago by hungmai1984
  0

• Create and query an index of many human genomes?

  #45 opened 2 years ago by jeremymsimon
  0

• xz-5.2.2.tar.gz: FAILED

  #38 opened 2 years ago by mmpust
  2

• Would Pufferfish index and align be more efficient if I merged each genome into a single contig and FASTA entry per genome?

  #43 opened 2 years ago by hermidalc
  1

• Cedar segfaults with SAM files

  #44 opened 2 years ago by hermidalc
  1

• PuffAligner significantly slower at mapping and thread usage is much less than specified when running with `--compressedOutput`

  #42 opened 2 years ago by hermidalc
  1

• Align command fails or shows help when options aren't in a specific order

  #41 opened 2 years ago by hermidalc
  1

• Output unmapped reads

  #40 opened 2 years ago by hermidalc
  0

• installing without root

  #27 opened 3 years ago by ksahlin
  13

• Pufferfish doesn't build within a conda environment (which has all the prerequisites) due to failed build of tslib from SeqLib

  #34 opened 2 years ago by hermidalc
  9

• Parallelize fixFasta

  #39 opened 2 years ago by hermidalc
  0

• Pufferfish index `--decoys <decoy_list>` option doesn't tell you how to provide a list of FASTA files

  #36 opened 2 years ago by hermidalc
  3

• Pufferfish index decoy option fixFasta doesn't recognize FASTA header(s) and fails

  #37 opened 2 years ago by hermidalc
  2

• Improve the help message, remove duplicate option descriptions, and get clarify options with the same flag

  #18 opened 4 years ago by nh13
  2

• Add description to help that pufferfish index supports gzipped FASTA reference file

  #35 opened 2 years ago by hermidalc
  0

• No executable after installing

  #32 opened 3 years ago by HenryYihengXu
  1

• [Compile error] cannot open output file cedar: Is a directory

  #31 opened 3 years ago by enricorox
  0

• Puffaligner fasta file

  #30 opened 3 years ago by nayeon1994
  1

• kquery, missing command

  #28 opened 3 years ago by chklopp
  28

• Please consider converting ExternalProject_Add to git submodules

  #29 opened 3 years ago by yurivict
  0

• Built-in FindTBB.cmake fails to find OpenTBB-2021.3.0

  #26 opened 3 years ago by yurivict
  3

• Puffaligner doesn't map read pairs to different references

  #23 opened 4 years ago by apcamargo
  2

• [Question] Effect of the 'genomicReads' parameter

  #22 opened 4 years ago by apcamargo
  1

• [Suggestion] Allow output to stdout

  #21 opened 4 years ago by apcamargo
  2

• Clarify usage for genome alignment

  #20 opened 4 years ago by ssadedin
  2

• Support interleaved paired end FASTQs

  #19 opened 4 years ago by nh13
  1

• Align without the "-o" option should just output to standard output

  #17 opened 4 years ago by nh13
  1

• make install does not work, pufferfish binary segfaults

  #15 opened 5 years ago by mathog
  20

• FindJemalloc.cmake does not work on CentOS 8

  #14 opened 5 years ago by mathog
  0

• Building an index using `salmon index` seems stuck at twopaco step

  #12 opened 5 years ago by dombraccia
  2

• pufferfish for assembly

  #3 opened 5 years ago by SilasK
  1

• Pufferfish Dependency: Need Help

  #4 opened 5 years ago by ruhulsbu
  1

• Pufferfish output files

  #7 opened 5 years ago by lutzkaro
  0

• "Index requested greater than vector's size" when loading pufferfish index using salmon v1.0

  #8 opened 5 years ago by mdshw5
  22

• fixfasta binary

  #5 opened 6 years ago by genomax
  6