Debian Patches

Status for pbsuite/15.8.24+dfsg-7

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

All known versions for source package 'pbsuite'

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