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Current Dev Version
Removed old executables:
MakeOverlapTable.py
MakeReciprocal.py
Polish.py
OLCAssembly.py
chunkyBlasr.py
Added --reportContigs to spots so that you can see the contig created
that called your spot if you want. By default it's off.
Added downsampling to Honey.py asm instead of failing when too many
reads were present. - and only for Illumina reads
Added new parameters for minimum gap inflation size for Jelly
Fixed an error where we weren't correctly using the -sa index for
Jelly mapping across all jobs
Corrected an error where single extend from 5' end captured gap
filling wasn't having the consensus bases correctly placed
PBSuite_15.2.20.p1
Quick patch for bugs.
-- GAPLIMIT Exception is fixed
File "PBSuite_15.2.20/bin/Collection.py", line 181, in getSequence
if gapLen < self.GAPINFLATE:
AttributeError: FillingMetrics instance has no attribute 'GAPINFLATE'
Safety for sawriter
If sawriter wasn't in the environment, the setup stage executed
silently when it should have raised errors.
The mapping stage now ensures the reference.sa exists, if not, it's
excluded from the blasr parameters. This will just make mapping
slower, not crash.
PBSuite_15.2.20
Utils
Command Runner now actually kills timed out forked processes.
Added bamToFastq.py and fixed bamToFastq so that it
reverse-compliments sequences
BamStat.py now has a prettier report and can read from sys.stdin
(e.g. samtools view input.bam 15:19428-19692 | BamStat.py)
PBHoney
Spots has been refactored to be faster, more informative, and a
more accurate
Spots now calls a consensus and gets a more accurate breakpoint.
Spots also reports strand counts
Spots also faster, though I also made a method that is optional
to use that goes much slower but is much cleaner pysam code.
Spots now throws in genotype information
Removed recallSpots.py. this is now inside of Honey.py spots with
--hon option
Extreme Multiprocessing -- PBHoney is now multiprocessed and has
splitting options with the --chrom parameter.
Tails and spots checks sort order and throws up some warning
bampie now adds PG information to your output.tails.bam header
Tails now uses default buffer of 1kb
Tails now looks to see if Bread.anno == Bread.anno before clustering.
This should prevent the '*' complex behavior
Mapping through pie uses different defualt blasr parameters
Mapping through pie has utility for running the initial mapping step
including creating chunks for you (see docs for details)
Spots now has the option of producing a readFile
Spots doesn't allow MapQ below --minMapQ count for discovery or
refinement
ComplexResolver -- Overlapping tail events are often indicative of a
more complex sample structure. This program resolves those
break-points to find a non-local annotation of the sample's
structure
Tails is now more memory efficient by parsing per-chromosome
Spots/Force now uses sizes and a delta to and collapse for potentially
spurious matches
Spots is now a little faster thanks to the collapse described above
Spots now reports a z-score for the significance of the intra-read
discordance that led to the spot's evaluation
PBJelly
Setup no longer has the noRename option.
Fixed bug in Extraction.py when a networkx version number like "1.9.1"
would break the code
Added parameter to Collection.py so that the min-gap size (gapInflate)
can be set (by default it has been 25)
ToDo/Coming Soon:
Complex Resolver Documentation
Need to split when you make subdirectories for gaps.
Pie automatically loading unmapped reads into your .sam/.bam
Pie fails when a there are no tails to be mapped. Need to make sure
the output file is actually created. (See "No Tails" ... exit)
Begin using pyvcf... I'll be outputing proper vcfs soon
Using SAM mate information properly (e.g. adding the fields for next)
PpPiPeIpIiIeEpEiEe
Merging Spots/Tails Calling (keep modules separate, but allow a
joint-calling procedure)
Haplotyping
Easy/well documented Annotation Pipeline
Add tails to Annotation Pipeline
Improve Force results format
All documentation needs to be improved. Honey is pretty complex now.
Honey asm downsampling needs to correctly choose 'best' reads instead of
random sample
Honey asm fetch
I need to fix the fetching logic for all but phrap - can i not pull
out that functionality? Also it's gotten kinda messy
I guess now that I fetch only around breakpoints, I don't really need
the max-span parameter.
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