Add paired fastq argument to transformFragments

[heuermh]

No description provided.

[AmplabJenkins]

Refer to this link for build results (access rights to CI server needed):
https://amplab.cs.berkeley.edu/jenkins//job/ADAM-prb/3163/

Build result: FAILURE

[...truncated 911 B...]Wiping out workspace first.Cloning the remote Git repositoryCloning repository https://github.com/bigdatagenomics/adam.git > git init /home/jenkins/workspace/ADAM-prb # timeout=10Using reference repository: /home/jenkins/gitcaches/adam.referenceFetching upstream changes from https://github.com/bigdatagenomics/adam.git > git --version # timeout=10 > git --version # 'git version 2.25.1' > git fetch --tags --force --progress -- https://github.com/bigdatagenomics/adam.git +refs/heads/:refs/remotes/origin/ # timeout=15 > git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=10 > git config --add remote.origin.fetch +refs/heads/:refs/remotes/origin/ # timeout=10 > git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=10Fetching upstream changes from https://github.com/bigdatagenomics/adam.git > git fetch --tags --force --progress -- https://github.com/bigdatagenomics/adam.git +refs/pull/:refs/remotes/origin/pr/ # timeout=15 > git rev-parse 0d53586^{commit} # timeout=10Checking out Revision 0d53586 (detached) > git config core.sparsecheckout # timeout=10 > git checkout -f 0d53586 # timeout=10Commit message: "Add paired fastq argument to transformFragments." > git rev-list --no-walk c489feb # timeout=10Triggering ADAM-prb » 3.2.1,2.12,3.0.2,ubuntuADAM-prb » 3.2.1,2.12,3.0.2,ubuntu completed with result FAILURENotifying endpoint with url 'https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'Setting status of 0d53586 to FAILURE with url https://amplab.cs.berkeley.edu/jenkins/job/ADAM-prb/3163/ and message: 'Build finished. '

[AmplabJenkins]

Refer to this link for build results (access rights to CI server needed):
https://amplab.cs.berkeley.edu/jenkins//job/ADAM-prb/3164/

Build result: FAILURE

[...truncated 911 B...]Wiping out workspace first.Cloning the remote Git repositoryCloning repository https://github.com/bigdatagenomics/adam.git > git init /home/jenkins/workspace/ADAM-prb # timeout=10Using reference repository: /home/jenkins/gitcaches/adam.referenceFetching upstream changes from https://github.com/bigdatagenomics/adam.git > git --version # timeout=10 > git --version # 'git version 2.25.1' > git fetch --tags --force --progress -- https://github.com/bigdatagenomics/adam.git +refs/heads/:refs/remotes/origin/ # timeout=15 > git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=10 > git config --add remote.origin.fetch +refs/heads/:refs/remotes/origin/ # timeout=10 > git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=10Fetching upstream changes from https://github.com/bigdatagenomics/adam.git > git fetch --tags --force --progress -- https://github.com/bigdatagenomics/adam.git +refs/pull/:refs/remotes/origin/pr/ # timeout=15 > git rev-parse e426e78^{commit} # timeout=10Checking out Revision e426e78 (detached) > git config core.sparsecheckout # timeout=10 > git checkout -f e426e78 # timeout=10Commit message: "update doc" > git rev-list --no-walk 0d53586 # timeout=10Triggering ADAM-prb » 3.2.1,2.12,3.0.2,ubuntuADAM-prb » 3.2.1,2.12,3.0.2,ubuntu completed with result FAILURENotifying endpoint with url 'https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'Setting status of e426e78 to FAILURE with url https://amplab.cs.berkeley.edu/jenkins/job/ADAM-prb/3164/ and message: 'Build finished. '