Issues

• How splitcode prioritizes matches beyond position and length of match: edit distance and order of tags in the config file

  pachterlab/splitcode#56 · Filter by author bentyeh opened on Mar 7, 2026

• Reverse complement config option seems incompatible with tags from files

  pachterlab/splitcode#43 · Filter by author clintval opened on Sep 21, 2025

• How to trim after, instead of before, extraction

  pachterlab/splitcode#40 · Filter by author clintval opened on Sep 14, 2025

• splitcode to get the read index of matching sequences

  pachterlab/splitcode#36 · Filter by author BiotechPedro opened on Jul 15, 2025

• Test not running to completion on aarch64-linux

  bug
  pachterlab/splitcode#31 · Filter by author zimward opened on Jan 8, 2025
  4

  

• Have --keep be able to output into BAM files rather than FASTQ files

  enhancement
  pachterlab/splitcode#29 · Filter by author Yenaled opened on Dec 10, 2024
  

• Extract barcodes (sample and UMI) from read names

  enhancement
  pachterlab/splitcode#22 · Filter by author nh13 opened on Aug 1, 2024
  3

  

• Allow stitching together extraction sequences of different names and allow extraction of final barcode sequence

  enhancement
  pachterlab/splitcode#21 · Filter by author Yenaled opened on Jul 9, 2024

• allow subs to make a substitution to an empty string (i.e. delete the entire sequence)

  enhancement
  pachterlab/splitcode#20 · Filter by author Yenaled opened on Jul 8, 2024

• feature request: support unmapped BAMs as input

  enhancement
  pachterlab/splitcode#17 · Filter by author znorgaard opened on Jul 3, 2024
  1

• Long-read usage

  pachterlab/splitcode#16 · Filter by author mcortes-lopez opened on Jun 28, 2024
  1

• Counting all tag combinations and reads without tags

  enhancement
  pachterlab/splitcode#14 · Filter by author andreafratton opened on May 3, 2024
  1

• Feature request: Processing on multiple sets of FASTQ files

  pachterlab/splitcode#13 · Filter by author JohnMMa opened on Mar 22, 2024
  1