Bug 24117.  Uncomment two lines in the method onChunk in the KineticWorker class that follow the comment Copy mod identification data.  Without these lines, sites that are identified as containing a particular modification, such as m6A, will not be reported to the modifications.gff file.  This can, for example, cause motifFinder to miss known motifs.

[git-p4: depot-paths = "//depot/software/bioinformatics/tools/kineticsTools/": change = 129955]
bug 24050 - remove all pip related conditionals from the master Makefile
pbcore/GenomicConsensus/kineticsTools/pbaha/pbalign/pbbarcode/pbh5tools/pbsamtools

[git-p4: depot-paths = "//depot/software/bioinformatics/tools/kineticsTools/": change = 130184]
Bug 24117.
       Temporarily switch off traceback and python debugger in main function.   A switch was made at some point to use the argparse library.  The --help option results in (1) printing the help messages, and (2) exiting with system exit code 0.  Somehow, the way argparse does step (2) seems to result in a traceback message and the pdb being started up.

[git-p4: depot-paths = "//depot/software/bioinformatics/tools/kineticsTools/": change = 130375]
Bug 24117. Better error handling so a few cases where non-zero exit codes aren't returning 0. More file/dir validation at the argparse level. Added --pdb option. --help and --pdb work as expected.

[git-p4: depot-paths = "//depot/software/bioinformatics/tools/kineticsTools/": change = 130380]
Bug 24117. Validate required files in copyIpdSummaryDataSet.py.

[git-p4: depot-paths = "//depot/software/bioinformatics/tools/kineticsTools/": change = 130381]
Bug 24117. Update validation in ipdSummary to use chemistry params dir (not file).

[git-p4: depot-paths = "//depot/software/bioinformatics/tools/kineticsTools/": change = 130388]
Bug 24117. Fix another bug in input file argparse level validation in ipdSummary.py.

[git-p4: depot-paths = "//depot/software/bioinformatics/tools/kineticsTools/": change = 130413]
Bug 24117. Remove argparse validation from optional ouputs in ipdSummary.py.

[git-p4: depot-paths = "//depot/software/bioinformatics/tools/kineticsTools/": change = 130417]
Bug 24117.
       In an earlier change (130375), had mistakenly made reference a positional argument.   Currently, the reference is specified using --reference.   

[git-p4: depot-paths = "//depot/software/bioinformatics/tools/kineticsTools/": change = 130434]
bug 24328 - remove gatkdict

[git-p4: depot-paths = "//depot/software/bioinformatics/tools/kineticsTools/": change = 130496]
Remove --refId argument, replace with more capable --refContig/-w argument

Accepts full (FASTA) name of contig, or multiple such names (comma-separated)

[Tracking bug 23893]

[git-p4: depot-paths = "//depot/software/bioinformatics/tools/kineticsTools/": change = 130513]
bug 24050 - refactoring regarding pip-install

[git-p4: depot-paths = "//depot/software/bioinformatics/tools/kineticsTools/": change = 130546]
bug 24050 - bad idea to redirect fd in Makefile, not robust.

[git-p4: depot-paths = "//depot/software/bioinformatics/tools/kineticsTools/": change = 130550]
Bug 24117.  Reproduce results of Medaka fish genome paper by Morishita et al. using ipdSummary.py.  When the --useLDA flag is set, an extra column, Ca5C, appears in the modifications.csv output.  The column contains a score for each CG site.  A negative score indicates that the site is estimated to be un-methylated.   The LDA classifier used here was trained using a small subset of the C2-C2 data provided with the paper in 2013.  The classifer is not expected to work for data collected using a different chemistry.  A simple R function that can be used along with these scores to estimate hypo-methylated region boundaries can be found here:  /home/UNIXHOME/obanerjee/new_test/regionBoundaries.R.   This function takes in a list of scores and a minimum region length, and returns a list of start and stop indices.  

[git-p4: depot-paths = "//depot/software/bioinformatics/tools/kineticsTools/": change = 130689]
Bug 24117.  Correcting a mistake I made in an earlier submission (130689).

[git-p4: depot-paths = "//depot/software/bioinformatics/tools/kineticsTools/": change = 130709]
ipdSummary accepts PacBio "ref000001"-style contig names in -w

[Tracking bug 23893]

[git-p4: depot-paths = "//depot/software/bioinformatics/tools/kineticsTools/": change = 131370]
       Give copyIpdSummaryDataset a mode for merging files

       To use it to merge the dataset files, use --mergefile <output.h5>

       [Bug 24720]

[git-p4: depot-paths = "//depot/software/bioinformatics/tools/kineticsTools/": change = 131504]
Add .gitignore

[Tracking bug 23893]

[git-p4: depot-paths = "//depot/software/bioinformatics/tools/kineticsTools/": change = 131517]
-W (contig list file) for kineticsTools

[Tracking bug 23893]

[git-p4: depot-paths = "//depot/software/bioinformatics/tools/kineticsTools/": change = 131518]
Permissions +x

[Tracking bug 23893]

[git-p4: depot-paths = "//depot/software/bioinformatics/tools/kineticsTools/": change = 131519]