| Patch | Description | Author | Forwarded | Bugs | Origin | Last update |
|---|---|---|---|---|---|---|
| fix-syntax-error.patch | Fix syntax error in pbbanana that prevents byte-compilation | Afif Elghraoui <afif@ghraoui.name> | no | 2015-12-12 | ||
| intervaltree-import-statement.patch | Fix intervaltree_bio import statement for successor project As mentioned on upstream's help forums [1], the original import statement here refers to the PyInterval package. That has been succeeded by intervaltree-bio. This patch adjusts the import statement to work with the successor package. . 1. http://sourceforge.net/p/pb-jelly/discussion/pbhtiks/thread/05f86d70/#fa4b |
Afif Elghraoui <afif@ghraoui.name> | no | 2015-12-12 | ||
| fix-example.patch | Adjust pbhoney example script for Debian * Use /bin/sh rather than /bin/bash (unnecessarily) * s/Honey.py/Honey/ * Fix error in example (reference parameter doesn't exist for one command but is required for another) * Replace sam2bam script (not packaged) with the actual samtools commands |
Afif Elghraoui <afif@ghraoui.name> | no | 2016-02-08 | ||
| fix-shebang-lines.patch | Fix shebang lines Fix invalid paths and replace usr/bin/env python with usr/bin/python. | Afif Elghraoui <afif@debian.org> | no | 2018-02-08 | ||
| blasr-5.patch | Update interface to blasr 5 blasr 5.1 and up began following the GNU convention for command-line flags. | Afif Elghraoui <afif@debian.org> | yes | debian upstream | 2016-12-11 | |
| intermediate-reads-files.patch | work around blasr 5's strict fasta/fastq header requirement blasr 5 can only produce sam/bam output if the fasta/fastq header is "PacBio compatible", or in the format <string>/<number>/<number>_<number>. See https://github.com/PacificBiosciences/blasr/issues/312#issuecomment-269055488 If blasr's input requirements for fasta and fastq files can be relaxed, this patch can be dropped. Alternatively, pbsuite could be revised to not store results in the fastq headers, but that is a more intrusive change. |
Afif Elghraoui <afif@debian.org> | yes | debian upstream | 2016-12-28 | |
| 2to3.patch | no | |||||
| fix_py3.patch | fix some py2 to py3 port | Olivier Sallou <osallou@debian.org> | no | |||
| python3.12-syntax.patch | Fix Python3.12 string syntax | Andreas Tille <tille@debian.org> | no | debian | 2024-06-09 |