Patch |
File delta |
Description |
fix syntax error.patch | (download) |
pbsuite/banana/SeqAsm.py |
4 2 + 2 - 0 !
1 file changed, 2 insertions(+), 2 deletions(-) |
fix syntax error in pbbanana that prevents byte-compilation
|
intervaltree import statement.patch | (download) |
pbsuite/honey/ComplexResolver.py |
2 1 + 1 - 0 !
1 file changed, 1 insertion(+), 1 deletion(-) |
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
|
fix example.patch | (download) |
docs/honeyExample/workflow.sh |
12 7 + 5 - 0 !
1 file changed, 7 insertions(+), 5 deletions(-) |
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
|
fix shebang lines.patch | (download) |
pbsuite/banana/MakeOverlapTable.py |
2 1 + 1 - 0 !
pbsuite/banana/MakeReciprocal.py |
2 1 + 1 - 0 !
pbsuite/banana/OLCAssembly.py |
2 1 + 1 - 0 !
pbsuite/banana/Polish.py |
2 1 + 1 - 0 !
pbsuite/banana/chunkyBlasr.py |
2 1 + 1 - 0 !
pbsuite/honey/ComplexResolver.py |
2 1 + 1 - 0 !
pbsuite/honey/Force.py |
2 1 + 1 - 0 !
pbsuite/honey/HSpots.py |
2 1 + 1 - 0 !
pbsuite/honey/HSpots.pyx |
2 1 + 1 - 0 !
pbsuite/honey/Honey.py |
2 1 + 1 - 0 !
pbsuite/honey/TGraf.py |
2 1 + 1 - 0 !
pbsuite/honey/bakH.py |
2 1 + 1 - 0 !
pbsuite/honey/bampie.py |
2 1 + 1 - 0 !
pbsuite/honey/massivePhrap.py |
2 1 + 1 - 0 !
pbsuite/honey/realign.py |
2 1 + 1 - 0 !
pbsuite/honey/recallSpots.py |
2 1 + 1 - 0 !
pbsuite/honey/spotH5Merge.py |
2 1 + 1 - 0 !
pbsuite/honey/spotH5dump.py |
2 1 + 1 - 0 !
pbsuite/honey/spotToBed.py |
2 1 + 1 - 0 !
pbsuite/honey/spotToVCF.py |
2 1 + 1 - 0 !
pbsuite/jelly/Assembly.py |
2 1 + 1 - 0 !
pbsuite/jelly/Collection.py |
2 1 + 1 - 0 !
pbsuite/jelly/Extraction.py |
2 1 + 1 - 0 !
pbsuite/jelly/Jelly.py |
2 1 + 1 - 0 !
pbsuite/jelly/QFix.py |
2 1 + 1 - 0 !
pbsuite/jelly/Setup.py |
2 1 + 1 - 0 !
pbsuite/jelly/Support.py |
2 1 + 1 - 0 !
pbsuite/jelly/m4pie.py |
2 1 + 1 - 0 !
pbsuite/utils/BamStat.py |
2 1 + 1 - 0 !
pbsuite/utils/bamToFastq.py |
2 1 + 1 - 0 !
pbsuite/utils/blasrToBed.py |
2 1 + 1 - 0 !
pbsuite/utils/fakeQuals.py |
2 1 + 1 - 0 !
pbsuite/utils/fastqDivide.py |
2 1 + 1 - 0 !
pbsuite/utils/fastqSplit.py |
2 1 + 1 - 0 !
pbsuite/utils/longCCSCombine.py |
2 1 + 1 - 0 !
pbsuite/utils/mapStats.py |
2 1 + 1 - 0 !
pbsuite/utils/mergeFaQu.py |
2 1 + 1 - 0 !
pbsuite/utils/quickN50.py |
2 1 + 1 - 0 !
pbsuite/utils/readSummary.py |
2 1 + 1 - 0 !
pbsuite/utils/summarizeAssembly.py |
2 1 + 1 - 0 !
pbsuite/utils/vcfTemplates/spotToVCF.py |
2 1 + 1 - 0 !
41 files changed, 41 insertions(+), 41 deletions(-) |
fix shebang lines
Fix invalid paths and replace usr/bin/env python with usr/bin/python.
|
blasr 5.patch | (download) |
docs/TemplateProtocol.xml |
2 1 + 1 - 0 !
docs/jellyExample/Protocol.xml |
2 1 + 1 - 0 !
pbsuite/banana/Banana.py |
4 2 + 2 - 0 !
pbsuite/banana/OLCAssembly.py |
6 3 + 3 - 0 !
pbsuite/banana/Polish.py |
2 1 + 1 - 0 !
pbsuite/banana/chunkyBlasr.py |
4 2 + 2 - 0 !
pbsuite/honey/HSpots.py |
16 8 + 8 - 0 !
pbsuite/honey/HSpots.pyx |
2 1 + 1 - 0 !
pbsuite/honey/Valid.py |
2 1 + 1 - 0 !
pbsuite/honey/bakH.py |
4 2 + 2 - 0 !
pbsuite/honey/bampie.py |
30 15 + 15 - 0 !
pbsuite/jelly/Assembly.py |
4 2 + 2 - 0 !
pbsuite/jelly/QFix.py |
2 1 + 1 - 0 !
pbsuite/jelly/Stages.py |
4 2 + 2 - 0 !
pbsuite/jelly/m4pie.py |
4 2 + 2 - 0 !
15 files changed, 44 insertions(+), 44 deletions(-) |
update interface to blasr 5
blasr 5.1 and up began following the GNU convention for command-line flags.
|
intermediate reads files.patch | (download) |
pbsuite/honey/bampie.py |
10 5 + 5 - 0 !
pbsuite/jelly/m4pie.py |
10 5 + 5 - 0 !
2 files changed, 10 insertions(+), 10 deletions(-) |
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.
|
2to3.patch | (download) |
pbsuite/banana/Banana.py |
10 5 + 5 - 0 !
pbsuite/banana/MakeOverlapTable.py |
2 1 + 1 - 0 !
pbsuite/banana/MakeReciprocal.py |
4 2 + 2 - 0 !
pbsuite/banana/OLCAssembly.py |
14 7 + 7 - 0 !
pbsuite/banana/Polish.py |
12 6 + 6 - 0 !
pbsuite/banana/SeqAsm.py |
6 3 + 3 - 0 !
pbsuite/honey/Force.py |
2 1 + 1 - 0 !
pbsuite/honey/HSpots.py |
16 8 + 8 - 0 !
pbsuite/honey/Honey.py |
2 1 + 1 - 0 !
pbsuite/honey/SVMachines.py |
10 5 + 5 - 0 !
pbsuite/honey/TGraf.py |
20 10 + 10 - 0 !
pbsuite/honey/Valid.py |
4 2 + 2 - 0 !
pbsuite/honey/bakH.py |
18 9 + 9 - 0 !
pbsuite/honey/bampie.py |
2 1 + 1 - 0 !
pbsuite/honey/massivePhrap.py |
8 4 + 4 - 0 !
pbsuite/honey/realign.py |
2 1 + 1 - 0 !
pbsuite/honey/recallSpots.py |
6 3 + 3 - 0 !
pbsuite/honey/spotH5Merge.py |
12 6 + 6 - 0 !
pbsuite/honey/spotH5dump.py |
6 3 + 3 - 0 !
pbsuite/honey/spotToBed.py |
2 1 + 1 - 0 !
pbsuite/honey/spotToVCF.py |
2 1 + 1 - 0 !
pbsuite/jelly/Assembly.py |
16 8 + 8 - 0 !
pbsuite/jelly/Collection.py |
24 12 + 12 - 0 !
pbsuite/jelly/Extraction.py |
12 6 + 6 - 0 !
pbsuite/jelly/GetSubs.py |
4 2 + 2 - 0 !
pbsuite/jelly/Jelly.py |
6 3 + 3 - 0 !
pbsuite/jelly/QFix.py |
12 6 + 6 - 0 !
pbsuite/jelly/Support.py |
10 5 + 5 - 0 !
pbsuite/jelly/m4pie.py |
4 2 + 2 - 0 !
pbsuite/utils/BamStat.py |
46 23 + 23 - 0 !
pbsuite/utils/CommandRunner.py |
4 2 + 2 - 0 !
pbsuite/utils/FileHandlers.py |
53 26 + 27 - 0 !
pbsuite/utils/VCFIO.py |
6 3 + 3 - 0 !
pbsuite/utils/blasrToBed.py |
4 2 + 2 - 0 !
pbsuite/utils/fakeQuals.py |
2 1 + 1 - 0 !
pbsuite/utils/fastqSplit.py |
6 3 + 3 - 0 !
pbsuite/utils/longCCSCombine.py |
6 3 + 3 - 0 !
pbsuite/utils/mapStats.py |
72 36 + 36 - 0 !
pbsuite/utils/mergeFaQu.py |
2 1 + 1 - 0 !
pbsuite/utils/quickN50.py |
4 2 + 2 - 0 !
pbsuite/utils/readSummary.py |
6 3 + 3 - 0 !
pbsuite/utils/summarizeAssembly.py |
50 25 + 25 - 0 !
pbsuite/utils/vcfTemplates/spotToVCF.py |
2 1 + 1 - 0 !
43 files changed, 255 insertions(+), 256 deletions(-) |
---
|
fix_py3.patch | (download) |
pbsuite/honey/HSpots.py |
12 6 + 6 - 0 !
pbsuite/honey/TGraf.py |
5 2 + 3 - 0 !
pbsuite/utils/FileHandlers.py |
3 1 + 2 - 0 !
3 files changed, 9 insertions(+), 11 deletions(-) |
fix some py2 to py3 port
|