Fix Jenkins Eichler BAC test

[Tracking bug 23893]

[git-p4: depot-paths = "//depot/software/bioinformatics/tools/GenomicConsensus/": change = 129201]
Add window to log message

[Tracking bug 23893]

[git-p4: depot-paths = "//depot/software/bioinformatics/tools/GenomicConsensus/": change = 129360]
Get rid of the timestamp in the logging format

I have never found it useful

[Tracking bug 23893]

[git-p4: depot-paths = "//depot/software/bioinformatics/tools/GenomicConsensus/": change = 129361]
Don't bother outputting log of row numbers if we know we won't call consensus here

[Tracking bug 23893]

[git-p4: depot-paths = "//depot/software/bioinformatics/tools/GenomicConsensus/": change = 129362]
Bump default maxIterations to 40 (was 20)

This doesn't change anything in the common case, but seems to improve
convergence on amplicons-style datasets.

(For example, reduces convergence failures by another 50% on fluidigm
amplicons)

[Tracking bug 23893]

[git-p4: depot-paths = "//depot/software/bioinformatics/tools/GenomicConsensus/": change = 129363]
Fix cram test --- log format change

[Tracking bug 23893]

[git-p4: depot-paths = "//depot/software/bioinformatics/tools/GenomicConsensus/": change = 129371]
Fix it again (tony)

[Tracking bug 23893]

[git-p4: depot-paths = "//depot/software/bioinformatics/tools/GenomicConsensus/": change = 129373]
A couple more log format change fixes

[Tracking bug 23893]

[git-p4: depot-paths = "//depot/software/bioinformatics/tools/GenomicConsensus/": change = 129377]
Fix jenkins (Eichler BAC consensus improves more!)

[Tracking bug 23893]

[git-p4: depot-paths = "//depot/software/bioinformatics/tools/GenomicConsensus/": change = 129396]
Fix jenkins failure 1/3

[Tracking bug 23893]

[git-p4: depot-paths = "//depot/software/bioinformatics/tools/GenomicConsensus/": change = 129471]
Don't try to detect cycling based on the template identity alone.

The system includes the MappedReads as well, so running into the same
template does not mean we are necessarily going to fail to converge.

[Tracking bug 23893]

[git-p4: depot-paths = "//depot/software/bioinformatics/tools/GenomicConsensus/": change = 129605]
ConsensusCore API change: interval methods expect signed integers

[Tracking bug 23893]

[git-p4: depot-paths = "//depot/software/bioinformatics/tools/GenomicConsensus/": change = 129606]
Add flexibility in specifying the quiver parameter set (-p):

if the user provides a chemistry name instead of a complete parameter
spec, deal with it by looking up the best parameter set applicable for
that chemistry.

Also, "best" default has been changed to "auto"

[Tracking bug 23893]

[git-p4: depot-paths = "//depot/software/bioinformatics/tools/GenomicConsensus/": change = 129693]
Log parameter filename

[Tracking bug 23893]

[git-p4: depot-paths = "//depot/software/bioinformatics/tools/GenomicConsensus/": change = 129725]
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/GenomicConsensus/": change = 130184]
Fix cram tests (ConsensusCore change causes QV changes at contig edges)

[Tracking bug 23893]

[git-p4: depot-paths = "//depot/software/bioinformatics/tools/GenomicConsensus/": change = 130230]
Print PID in debug mode

[Tracking bug 23893]

[git-p4: depot-paths = "//depot/software/bioinformatics/tools/GenomicConsensus/": change = 130231]
Allow ConsensusCore > 0.7.0

[Tracking bug 23893]

[git-p4: depot-paths = "//depot/software/bioinformatics/tools/GenomicConsensus/": change = 130235]
Tweak two of the internal tests (ConsensusCore change)

[Tracking bug 23893]

[git-p4: depot-paths = "//depot/software/bioinformatics/tools/GenomicConsensus/": change = 130253]
Re-enable fluidigm amplicons test---which doesn't check anything yet at this time.

[Tracking bug 23893]

[git-p4: depot-paths = "//depot/software/bioinformatics/tools/GenomicConsensus/": change = 130271]