CHANGELOG.txt

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.