merge most recent from master

.gitignore

@@ -22,6 +22,7 @@ tests/testthat/JaBbA.empty.jj/
 tests/testthat/JaBbA.tier/
 tests/testthat/JaBbA.ism/
 tests/testthat/JaBbA.mem/
+tests/testthat/JaBbA.*/
 tests/testthat/JaBbA/
 tests/testthat/raw.prm
 tests/testthat/raw.sols.rds

.travis.yml

@@ -11,14 +11,30 @@ bioc_packages:
 - VariantAnnotation
 - DNAcopy
 - rtracklayer
+- Rsamtools
 before_install:
 - curl -OL $URL
 - mv jabba.tar.gz.gpg?dl=0 jabba.tar.gz.gpg
 - echo $JAB | sudo gpg --passphrase-fd 0 jabba.tar.gz.gpg
 - mkdir $HOME/my.cplex && tar -xvzf jabba.tar.gz --directory $HOME/my.cplex/
+- wget https://github.com/samtools/samtools/releases/download/1.6/samtools-1.6.tar.bz2
+- tar -vxjf samtools-1.6.tar.bz2
+- cd samtools-1.6
+- make
+- cd ..
+- export PATH=samtools-1.6/:$PATH
 - curl -OL https://raw.githubusercontent.com/craigcitro/r-travis/master/scripts/travis-tool.sh
 - chmod 755 ./travis-tool.sh
-script: ./travis-tool.sh run_tests
+install:
+- ./travis-tool.sh install_github mskilab/bamUtils
+- ./travis-tool.sh install_github mskilab/gUtils
+- ./travis-tool.sh install_github mskilab/gTrack
+- ./travis-tool.sh install_github mskilab/gGnome
+script:
+- "Rscript -e 'devtools::install_bioc(\"copynumber\")'"
+- "Rscript -e 'setRepositories(graphics = FALSE, ind = 1:6);install.packages(\"sequenza\")'"
+- "Rscript -e 'devtools::install()'"
+- "./travis-tool.sh run_tests"
 after_failure:
 - "./travis-tool.sh dump_logs"
 after_success:
@@ -35,3 +51,4 @@ env:
   - _R_CHECK_TESTS_NLINES_=0
   - R_REMOTES_NO_ERRORS_FROM_WARNINGS=TRUE
   - _R_CHECK_FORCE_SUGGESTS_=false
+  - secure: X/MLEu5WhqFG9gFs9lN+TNwZSXA9Lv+4J6uCo2WmtKB1lmujN5hcZb4AiylkblHC2YxajhsLskhE5Fnx04SbeqzPv0fGmIKFY6RT1fNlLFrp9h5kDHiy9DzbHQPW2ocU4KT2rExWpLCttplVLTmBed6AnhCKy8pO5Flodm4mdET/ioWtxjbD8VHHqsCnieMeYkeU004OMmiPZjM7oeUIMgV3lOeA0Sk1DEVSVtGgNg11vTmqlBqi247mddXyhT+UMofPpjleGlhVzakPGASV9+mSaG5vN+rqwd64CTLottdb4E3+ASWmWMPQe9k9Lw9lbnus+OenebKTbzONjwz0dF8sbIHuElbbubZLxXEBtHJv6+ZILZnZFYg99NDtLQTT//ZVbQssPM6OP4TZfKduSvcrY5HJX0TDZxe4SY6DEJG6NSvQFJEP+lAv4CEtfodnHwU0Qh7jH5lIp7Sw4lyG/Fpto8KUXL8oV5lo3T5o1JjQ6SJES69ApGUUEBVhHaygtJg4VS+Wzx+Gk7LhpBx9S9+FlQaXqjSvV1uQqB/JMF700IMXvkheZDJvVH0+WT7FSEyj/G2Do7karPYZFYTVB+54Glx59vJ0dhIV61LHbLn7P8YAM0ntPTDxnwry2n2HhaiHuPbK23dhzFPY0tL5IP3rnijwJ5S1YadKNA17S/U=

DESCRIPTION

@@ -10,15 +10,18 @@ Remotes:
   bioc::3.10/GenomicRanges,
   bioc::3.10/rtracklayer,
   bioc::3.10/VariantAnnotation,
+  bioc::3.10/copynumber,
+  github::mskilab/bamUtils,
   github::mskilab/gUtils,
   github::mskilab/gTrack,
+  github::mskilab/gChain,
   github::mskilab/gGnome
 Depends:
   R (>= 3.6.0),
-  gUtils, 
+  GenomicRanges,
+  gUtils,
   gTrack,
-  gGnome, 
-  GenomicRanges
+  gGnome
 Imports:
   data.table,
   Matrix,