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update picard 2.18.11 -> 2.20.3 (#977)

* update picard 2.18.11 -> 2.20.3

* remove certain characters from unit test input fasta that are disallowed by picard

commas, single quotes, etc.

* compare only reads in sam post-depletion

compare only reads in sam post-depletion, allowing us to ignore header differences due to varying versions of picard/samtools/htslib; remove related permutations of expected output from tests

* update expected output for depletion db build tests

* use regex to allow for flexible header comparison in picard test

* In TestFastqBam, resolve longstanding brittle test case

add new test assertion, "assertEqualSamHeaders" to address this inline ToDo for TestFastqBam(): "Note for developers: if you're fixing the tests to handle non-bugs (ie our testing here is too brittle), let's just replace a lot of this in the future with code that just reads the header, sorts it, and tests for equality of sorted values in the RG line (and stricter equality in the non-header lines). This is kind of hacky."

* add debug statements to install-viral-ngs.sh script

add debug statements to install-viral-ngs.sh Docker script

* install viral-ngs dependencies to separate conda env from base env

* let's try conda 4.7.10

* unpin conda-build and jinja2

* bump conda-build

* do not install gcc

* pin CONDA_R=3.4.1

* conda build --debug

* let's try pinning R to the latest since something is pulling it in?

* remove --debug from conda-build

* bump r version

required by GATK 3.8 conda package

* r-base

* r 3.5.1

* matplotlib 2.2.0 -> 2.2.4

* bedtools 2.27.1 -> 2.28.0

* blast 2.6.0 -> 2.7.1

* roll back test input to state of origin/master; add functions to util.file to sanitize fasta file IDs

fasta ID is sanitized for picard CreateSequenceDictionary to adhere to character set restrictions in SAM/BAM RNAME spec. see: https://github.com/samtools/hts-specs/pull/333

Roll back test input ... (continued)

2636 of 4394 branches covered (59.99%)

7410 of 10056 relevant lines covered (73.69%)

0.74 hits per line