s4hts/HTStream

Issues

• Issue in Common: Memory Leak in `check_open_r` (not closing file)

  #258 opened 5 months ago by dstreett
  2

• Compiling from source fails on Ubuntu 22.04.1

  #251 opened a year ago by amphioxus
  2

• munmap_chunk(): invalid pointer error

  #255 opened a year ago by jrlyen
  3

• pointer error in hts_Stats

  #249 opened a year ago by najoshi
  1

• "no such file or directory" error

  #254 opened a year ago by Emmashipman
  2

• Order of input files to hts_SeqScreener changes hits reported when R1/R2 lengths differ

  #253 opened a year ago by AstrobioMike
  0

• Remaining adapter sequence

  #252 opened 2 years ago by cdermita
  0

• Add to CutTrim, trim to length from 5' or 3'

  #246 opened 3 years ago by msettles
  0

• SuperDeduper ignoring reads

  #238 opened 3 years ago by channsoden
  6

• citation?

  #245 opened 3 years ago by Tgrandis
  2

• hts_LengthFilter is missing from the documentation!

  #244 opened 3 years ago by samhunter
  0

• How to cite HTStream? :-)

  #243 opened 3 years ago by mickey-spongebob
  2

• Version incorrect and CMAKE_PREFIX_PATH not working

  #242 opened 4 years ago by najoshi
  5

• hts_Primers - error message

  #241 opened 4 years ago by adamerum
  4

• Flag use

  #235 opened 4 years ago by emmadoughty
  1

• hts_Primers doesn't seem to read multi-fasta files correctly

  #239 opened 4 years ago by samhunter
  0

• Is "percentage-hits" calculated properly for SeqScreener?

  #237 opened 4 years ago by samhunter
  1

• -m (minLength) option removed from hts_QWindowTrim, but does not exist in hts_CutTrim

  #232 opened 4 years ago by marade
  3

• Feature downgrade actually, remove -a option from SuperD

  #231 opened 4 years ago by msettles
  0

• hts_Primer doesn't report fragments and basepairs_in

  #229 opened 4 years ago by msettles
  0

• Stats file format issue

  #221 opened 4 years ago by joe-angell
  6

• hts_SeqScreener enhancements for bigger references

  #227 opened 4 years ago by samhunter
  0

• make "unhandled" errrors that are expected to have improved messaging

  #222 opened 4 years ago by joe-angell
  0

• AND the biggie, move HTStream to a new Org as no-one involved is apart of IBEST anymore

  #208 opened 4 years ago by msettles
  20

• N-trimmer might have an overflow on Right bp trim

  #215 opened 4 years ago by msettles
  3

• Better 10X support (was Possibility to do QC only on one pair?)

  #172 opened 5 years ago by jenzopr
  7

• hts_SuperDeduper should mark duplicates by default, not remove them

  #171 opened 5 years ago by marade
  6

• MultiQC report support

  #207 opened 4 years ago by msettles
  0

• New documentation under master /doc

  #206 opened 4 years ago by msettles
  0

• Rework PolyATTrim to be "fragment" oriented parameters.

  #205 opened 4 years ago by msettles
  0

• multicore version of Overlapper and SeqScreener, SuperDeduper?

  #204 opened 4 years ago by msettles
  0

• Split screener across multifasta file

  #203 opened 4 years ago by msettles
  0

• What should be done about Novaseq base qualities?

  #174 opened 5 years ago by samhunter
  1

• New app hts_LengthFilter

  #196 opened 4 years ago by msettles
  1

• add log file arg to -A --append-stats-file so that we use either -A OR -L, but not both are needed

  #193 opened 4 years ago by msettles
  2

• Regex error

  #177 opened 4 years ago by pikabika
  4

• HTStream needs more informative logs

  #175 opened 4 years ago by samhunter
  2

• Should the HTStream version be included in the log file?

  #184 opened 4 years ago by samhunter
  2

• hts_PolyATTrim has three "-i" switches

  #166 opened 4 years ago by samhunter
  3

• N-trimmer add maxN parameter

  #164 opened 4 years ago by msettles
  1

• hts_PolyATTrim segfaults when run with a single input file

  #167 opened 5 years ago by samhunter
  0

• Add an option to hts_NTrimmer that simply discards any read with an N

  #176 opened 5 years ago by samhunter
  1

• symbol lookup error

  #169 opened 5 years ago by yingeddi2008
  3

• In SuperDeduper add ability to extract and use UMIs

  #165 opened 5 years ago by msettles
  0

• HTStream as a Singularity/Docker container

  #162 opened 5 years ago by germaine260
  9

• hts_SuperDeduper input filenames containing spaces not supported

  #160 opened 5 years ago by yhoogstrate
  7

• Add support for sam file format as input

  #157 opened 5 years ago by msettles
  0

• Interleaved output broken when one read is discarded by hts_QWindowTrim

  #149 opened 5 years ago by samhunter
  1

• Tab-delimited output of hts_Stats leads to unhandled exception

  #154 opened 5 years ago by jenzopr
  4

• Improvement Suggestion

  #150 opened 6 years ago by efratushava
  1