Package: pbsuite / 15.8.24+dfsg-3

Metadata

Package Version Patches format
pbsuite 15.8.24+dfsg-3 3.0 (quilt)

Patch series

view the series file
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.