Fix paired read viewing and bump deps

build/dojo-webpack-plugin-loader/dojo/dojo.js

@@ -1,4 +1,4 @@
-module.exports = function(userConfig, defaultConfig, global, window) { this.loaderVersion = "1.15.0"; (function(
+module.exports = function(userConfig, defaultConfig, global, window) { this.loaderVersion = "1.16.0"; (function(
 	userConfig,
 	defaultConfig
 ){

package.json

@@ -42,7 +42,7 @@
     "shelljs": "^0.7.8"
   },
   "devDependencies": {
-    "@gmod/bam": "^1.0.33",
+    "@gmod/bam": "^1.0.34",
     "@gmod/cram": "^1.5.3",
     "@gmod/gff": "^1.1.1",
     "@gmod/indexedfasta": "^1.0.11",

src/JBrowse/Store/SeqFeature/BAM.js

@@ -9,7 +9,7 @@ const BlobFilehandleWrapper = cjsRequire('../../Model/BlobFilehandleWrapper')
 class BamSlightlyLazyFeature {
     _get_id() { this.record.id() }
     _get_type() { return 'match'}
-    _get_score() { return this.record._get('mq')}
+    _get_score() { return this.record.get('mq')}
     _get_mapping_quality() { return this.record.mappingQuality}
     _get_flags() { return `0x${this.record.flags.toString(16)}`}
     _get_strand() { return this.record.isReverseComplemented() ? -1 : 1 }
@@ -52,7 +52,7 @@ class BamSlightlyLazyFeature {
     _get(field) {
         const methodName = `_get_${field}`
         if (this[methodName]) return this[methodName]()
-        else return this.record._get(field)
+        else return this.record.get(field)
     }
     get(field) {
         const methodName = `_get_${field.toLowerCase()}`

yarn.lock

@@ -157,10 +157,10 @@
   dependencies:
     arrify "^1.0.1"
 
-"@gmod/bam@^1.0.33":
-  version "1.0.33"
-  resolved "https://registry.yarnpkg.com/@gmod/bam/-/bam-1.0.33.tgz#9921e25a26d6e2dd1902ec165787d0d5623d1296"
-  integrity sha512-vfr3EHYL41ncHGgWc2ub33V3XUzAGjeG+2gQ77SKung7ZRoyAR54gmPalTPJK5sLE1qvj/KGOP52Ygng28Jw0Q==
+"@gmod/bam@^1.0.34":
+  version "1.0.34"
+  resolved "https://registry.yarnpkg.com/@gmod/bam/-/bam-1.0.34.tgz#6c9ba8f6d083c45a0ee82ef0f81534a5af0bba03"
+  integrity sha512-b59eqjPAN3/ZlfclfQIOKBlI2S23yVANEIIBnObM4/iPmE4JlWJqwyJpu8K+b7gpQQYqHmpRAxEyKiSvn6NTaA==
   dependencies:
     "@babel/runtime-corejs2" "^7.5.5"
     "@gmod/bgzf-filehandle" "^1.3.0"
@@ -2535,7 +2535,7 @@ [email protected], debug@^2.1.3, debug@^2.2.0, debug@^2.3.3, debug@^2.6.8, debug@^2.6.
   dependencies:
     ms "2.0.0"
 
-debug@^3.0.0, debug@^3.0.1, debug@^3.1.0, debug@^3.2.6:
+debug@^3.0.0, debug@^3.0.1, debug@^3.1.0:
   version "3.2.6"
   resolved "https://registry.yarnpkg.com/debug/-/debug-3.2.6.tgz#e83d17de16d8a7efb7717edbe5fb10135eee629b"
   integrity sha512-mel+jf7nrtEl5Pn1Qx46zARXKDpBbvzezse7p7LqINmdoIk8PYP5SySaxEmYv6TZ0JyEKA1hsCId6DIhgITtWQ==
@@ -2673,11 +2673,6 @@ detect-indent@^5.0.0:
   resolved "https://registry.yarnpkg.com/detect-indent/-/detect-indent-5.0.0.tgz#3871cc0a6a002e8c3e5b3cf7f336264675f06b9d"
   integrity sha1-OHHMCmoALow+Wzz38zYmRnXwa50=
 
-detect-libc@^1.0.2:
-  version "1.0.3"
-  resolved "https://registry.yarnpkg.com/detect-libc/-/detect-libc-1.0.3.tgz#fa137c4bd698edf55cd5cd02ac559f91a4c4ba9b"
-  integrity sha1-+hN8S9aY7fVc1c0CrFWfkaTEups=
-
 dev-null@^0.1.1:
   version "0.1.1"
   resolved "https://registry.yarnpkg.com/dev-null/-/dev-null-0.1.1.tgz#5a205ce3c2b2ef77b6238d6ba179eb74c6a0e818"
@@ -3662,13 +3657,6 @@ fs-extra@^7.0.0:
     jsonfile "^4.0.0"
     universalify "^0.1.0"
 
-fs-minipass@^1.2.5:
-  version "1.2.7"
-  resolved "https://registry.yarnpkg.com/fs-minipass/-/fs-minipass-1.2.7.tgz#ccff8570841e7fe4265693da88936c55aed7f7c7"
-  integrity sha512-GWSSJGFy4e9GUeCcbIkED+bgAoFyj7XF1mV8rma3QW4NIqX9Kyx79N/PF61H5udOV3aY1IaMLs6pGbH71nlCTA==
-  dependencies:
-    minipass "^2.6.0"
-
 fs-write-stream-atomic@^1.0.8:
   version "1.0.10"
   resolved "https://registry.yarnpkg.com/fs-write-stream-atomic/-/fs-write-stream-atomic-1.0.10.tgz#b47df53493ef911df75731e70a9ded0189db40c9"
@@ -4181,7 +4169,7 @@ hullabaloo-config-manager@^1.1.0:
     resolve-from "^3.0.0"
     safe-buffer "^5.0.1"
 
-[email protected], iconv-lite@^0.4.17, iconv-lite@^0.4.4:
+[email protected], iconv-lite@^0.4.17:
   version "0.4.24"
   resolved "https://registry.yarnpkg.com/iconv-lite/-/iconv-lite-0.4.24.tgz#2022b4b25fbddc21d2f524974a474aafe733908b"
   integrity sha512-v3MXnZAcvnywkTUEZomIActle7RXXeedOR31wwl7VlyoXO4Qi9arvSenNQWne1TcRwhCL1HwLI21bEqdpj8/rA==
@@ -4215,13 +4203,6 @@ ignore-by-default@^1.0.0:
   resolved "https://registry.yarnpkg.com/ignore-by-default/-/ignore-by-default-1.0.1.tgz#48ca6d72f6c6a3af00a9ad4ae6876be3889e2b09"
   integrity sha1-SMptcvbGo68Aqa1K5odr44ieKwk=
 
-ignore-walk@^3.0.1:
-  version "3.0.3"
-  resolved "https://registry.yarnpkg.com/ignore-walk/-/ignore-walk-3.0.3.tgz#017e2447184bfeade7c238e4aefdd1e8f95b1e37"
-  integrity sha512-m7o6xuOaT1aqheYHKf8W6J5pYH85ZI9w077erOzLje3JsB1gkafkAhHHY19dqjulgIZHFm32Cp5uNZgcQqdJKw==
-  dependencies:
-    minimatch "^3.0.4"
-
 ignore@^3.3.3, ignore@^3.3.5:
   version "3.3.10"
   resolved "https://registry.yarnpkg.com/ignore/-/ignore-3.3.10.tgz#0a97fb876986e8081c631160f8f9f389157f0043"
@@ -5379,21 +5360,6 @@ minimist@~0.0.1:
   resolved "https://registry.yarnpkg.com/minimist/-/minimist-0.0.10.tgz#de3f98543dbf96082be48ad1a0c7cda836301dcf"
   integrity sha1-3j+YVD2/lggr5IrRoMfNqDYwHc8=
 
-minipass@^2.6.0, minipass@^2.8.6, minipass@^2.9.0:
-  version "2.9.0"
-  resolved "https://registry.yarnpkg.com/minipass/-/minipass-2.9.0.tgz#e713762e7d3e32fed803115cf93e04bca9fcc9a6"
-  integrity sha512-wxfUjg9WebH+CUDX/CdbRlh5SmfZiy/hpkxaRI16Y9W56Pa75sWgd/rvFilSgrauD9NyFymP/+JFV3KwzIsJeg==
-  dependencies:
-    safe-buffer "^5.1.2"
-    yallist "^3.0.0"
-
-minizlib@^1.2.1:
-  version "1.3.3"
-  resolved "https://registry.yarnpkg.com/minizlib/-/minizlib-1.3.3.tgz#2290de96818a34c29551c8a8d301216bd65a861d"
-  integrity sha512-6ZYMOEnmVsdCeTJVE0W9ZD+pVnE8h9Hma/iOwwRDsdQoePpoX56/8B6z3P9VNwppJuBKNRuFDRNRqRWexT9G9Q==
-  dependencies:
-    minipass "^2.9.0"
-
 mississippi@^2.0.0:
   version "2.0.0"
   resolved "https://registry.yarnpkg.com/mississippi/-/mississippi-2.0.0.tgz#3442a508fafc28500486feea99409676e4ee5a6f"
@@ -5537,15 +5503,6 @@ natural-compare@^1.4.0:
   resolved "https://registry.yarnpkg.com/natural-compare/-/natural-compare-1.4.0.tgz#4abebfeed7541f2c27acfb29bdbbd15c8d5ba4f7"
   integrity sha1-Sr6/7tdUHywnrPspvbvRXI1bpPc=
 
-needle@^2.2.1:
-  version "2.4.0"
-  resolved "https://registry.yarnpkg.com/needle/-/needle-2.4.0.tgz#6833e74975c444642590e15a750288c5f939b57c"
-  integrity sha512-4Hnwzr3mi5L97hMYeNl8wRW/Onhy4nUKR/lVemJ8gJedxxUyBLm9kkrDColJvoSfwi0jCNhD+xCdOtiGDQiRZg==
-  dependencies:
-    debug "^3.2.6"
-    iconv-lite "^0.4.4"
-    sax "^1.2.4"
-
 [email protected]:
   version "0.6.2"
   resolved "https://registry.yarnpkg.com/negotiator/-/negotiator-0.6.2.tgz#feacf7ccf525a77ae9634436a64883ffeca346fb"
@@ -5630,22 +5587,6 @@ node-libs-browser@^2.2.1:
     util "^0.11.0"
     vm-browserify "^1.0.1"
 
-node-pre-gyp@*:
-  version "0.14.0"
-  resolved "https://registry.yarnpkg.com/node-pre-gyp/-/node-pre-gyp-0.14.0.tgz#9a0596533b877289bcad4e143982ca3d904ddc83"
-  integrity sha512-+CvDC7ZttU/sSt9rFjix/P05iS43qHCOOGzcr3Ry99bXG7VX953+vFyEuph/tfqoYu8dttBkE86JSKBO2OzcxA==
-  dependencies:
-    detect-libc "^1.0.2"
-    mkdirp "^0.5.1"
-    needle "^2.2.1"
-    nopt "^4.0.1"
-    npm-packlist "^1.1.6"
-    npmlog "^4.0.2"
-    rc "^1.2.7"
-    rimraf "^2.6.1"
-    semver "^5.3.0"
-    tar "^4.4.2"
-
 node-sass@^4.12.0:
   version "4.13.1"
   resolved "https://registry.yarnpkg.com/node-sass/-/node-sass-4.13.1.tgz#9db5689696bb2eec2c32b98bfea4c7a2e992d0a3"
@@ -5689,14 +5630,6 @@ nodeify@^1.0.1:
   dependencies:
     abbrev "1"
 
-nopt@^4.0.1:
-  version "4.0.1"
-  resolved "https://registry.yarnpkg.com/nopt/-/nopt-4.0.1.tgz#d0d4685afd5415193c8c7505602d0d17cd64474d"
-  integrity sha1-0NRoWv1UFRk8jHUFYC0NF81kR00=
-  dependencies:
-    abbrev "1"
-    osenv "^0.1.4"
-
 nopt@~1.0.10:
   version "1.0.10"
   resolved "https://registry.yarnpkg.com/nopt/-/nopt-1.0.10.tgz#6ddd21bd2a31417b92727dd585f8a6f37608ebee"
@@ -5731,40 +5664,19 @@ normalize-wheel@^1.0.1:
   resolved "https://registry.yarnpkg.com/normalize-wheel/-/normalize-wheel-1.0.1.tgz#aec886affdb045070d856447df62ecf86146ec45"
   integrity sha1-rsiGr/2wRQcNhWRH32Ls+GFG7EU=
 
-npm-bundled@^1.0.1:
-  version "1.1.1"
-  resolved "https://registry.yarnpkg.com/npm-bundled/-/npm-bundled-1.1.1.tgz#1edd570865a94cdb1bc8220775e29466c9fb234b"
-  integrity sha512-gqkfgGePhTpAEgUsGEgcq1rqPXA+tv/aVBlgEzfXwA1yiUJF7xtEt3CtVwOjNYQOVknDk0F20w58Fnm3EtG0fA==
-  dependencies:
-    npm-normalize-package-bin "^1.0.1"
-
 npm-install-package@~2.1.0:
   version "2.1.0"
   resolved "https://registry.yarnpkg.com/npm-install-package/-/npm-install-package-2.1.0.tgz#d7efe3cfcd7ab00614b896ea53119dc9ab259125"
   integrity sha1-1+/jz816sAYUuJbqUxGdyaslkSU=
 
-npm-normalize-package-bin@^1.0.1:
-  version "1.0.1"
-  resolved "https://registry.yarnpkg.com/npm-normalize-package-bin/-/npm-normalize-package-bin-1.0.1.tgz#6e79a41f23fd235c0623218228da7d9c23b8f6e2"
-  integrity sha512-EPfafl6JL5/rU+ot6P3gRSCpPDW5VmIzX959Ob1+ySFUuuYHWHekXpwdUZcKP5C+DS4GEtdJluwBjnsNDl+fSA==
-
-npm-packlist@^1.1.6:
-  version "1.4.8"
-  resolved "https://registry.yarnpkg.com/npm-packlist/-/npm-packlist-1.4.8.tgz#56ee6cc135b9f98ad3d51c1c95da22bbb9b2ef3e"
-  integrity sha512-5+AZgwru5IevF5ZdnFglB5wNlHG1AOOuw28WhUq8/8emhBmLv6jX5by4WJCh7lW0uSYZYS6DXqIsyZVIXRZU9A==
-  dependencies:
-    ignore-walk "^3.0.1"
-    npm-bundled "^1.0.1"
-    npm-normalize-package-bin "^1.0.1"
-
 npm-run-path@^2.0.0:
   version "2.0.2"
   resolved "https://registry.yarnpkg.com/npm-run-path/-/npm-run-path-2.0.2.tgz#35a9232dfa35d7067b4cb2ddf2357b1871536c5f"
   integrity sha1-NakjLfo11wZ7TLLd8jV7GHFTbF8=
   dependencies:
     path-key "^2.0.0"
 
-"npmlog@0 || 1 || 2 || 3 || 4", npmlog@^4.0.0, npmlog@^4.0.2:
+"npmlog@0 || 1 || 2 || 3 || 4", npmlog@^4.0.0:
   version "4.1.2"
   resolved "https://registry.yarnpkg.com/npmlog/-/npmlog-4.1.2.tgz#08a7f2a8bf734604779a9efa4ad5cc717abb954b"
   integrity sha512-2uUqazuKlTaSI/dC8AzicUck7+IrEaOnN/e0jd3Xtt1KcGpwx30v50mL7oPyr/h9bL3E4aZccVwpwP+5W9Vjkg==
@@ -5968,7 +5880,7 @@ os-tmpdir@^1.0.0, os-tmpdir@^1.0.1, os-tmpdir@~1.0.1, os-tmpdir@~1.0.2:
   resolved "https://registry.yarnpkg.com/os-tmpdir/-/os-tmpdir-1.0.2.tgz#bbe67406c79aa85c5cfec766fe5734555dfa1274"
   integrity sha1-u+Z0BseaqFxc/sdm/lc0VV36EnQ=
 
-osenv@0, osenv@^0.1.4:
+osenv@0:
   version "0.1.5"
   resolved "https://registry.yarnpkg.com/osenv/-/osenv-0.1.5.tgz#85cdfafaeb28e8677f416e287592b5f3f49ea410"
   integrity sha512-0CWcCECdMVc2Rw3U5w9ZjqX6ga6ubk1xDVKxtBQPK7wis/0F2r9T6k4ydGYhecl7YUBxBVxhL5oisPsNxAPe2g==
@@ -6626,7 +6538,7 @@ [email protected]:
   resolved "https://registry.yarnpkg.com/raw-loader/-/raw-loader-0.5.1.tgz#0c3d0beaed8a01c966d9787bf778281252a979aa"
   integrity sha1-DD0L6u2KAclm2Xh793goElKpeao=
 
-rc@^1.0.1, rc@^1.1.6, rc@^1.2.1, rc@^1.2.7:
+rc@^1.0.1, rc@^1.1.6, rc@^1.2.1:
   version "1.2.8"
   resolved "https://registry.yarnpkg.com/rc/-/rc-1.2.8.tgz#cd924bf5200a075b83c188cd6b9e211b7fc0d3ed"
   integrity sha512-y3bGgqKj3QBdxLbLkomlohkvsA8gdAiUQlSBJnBhfn+BPxg4bc62d8TcBW15wavDfgexCgccckhcZvywyQYPOw==
@@ -7063,11 +6975,6 @@ sass-loader@^6.0.7:
     neo-async "^2.5.0"
     pify "^3.0.0"
 
-sax@^1.2.4:
-  version "1.2.4"
-  resolved "https://registry.yarnpkg.com/sax/-/sax-1.2.4.tgz#2816234e2378bddc4e5354fab5caa895df7100d9"
-  integrity sha512-NqVDv9TpANUjFm0N8uM5GxL36UgKi9/atZw+x7YFnQ8ckwFGKrl4xX4yWtrey3UJm5nP1kUbnYgLopqWNSRhWw==
-
 schema-utils@^0.4.5:
   version "0.4.7"
   resolved "https://registry.yarnpkg.com/schema-utils/-/schema-utils-0.4.7.tgz#ba74f597d2be2ea880131746ee17d0a093c68187"
@@ -7714,19 +7621,6 @@ tar@^2.0.0:
     fstream "^1.0.12"
     inherits "2"
 
-tar@^4.4.2:
-  version "4.4.13"
-  resolved "https://registry.yarnpkg.com/tar/-/tar-4.4.13.tgz#43b364bc52888d555298637b10d60790254ab525"
-  integrity sha512-w2VwSrBoHa5BsSyH+KxEqeQBAllHhccyMFVHtGtdMpF4W7IRWfZjFiQceJPChOeTsSDVUpER2T8FA93pr0L+QA==
-  dependencies:
-    chownr "^1.1.1"
-    fs-minipass "^1.2.5"
-    minipass "^2.8.6"
-    minizlib "^1.2.1"
-    mkdirp "^0.5.0"
-    safe-buffer "^5.1.2"
-    yallist "^3.0.3"
-
 tenacious-fetch@^2.1.0:
   version "2.2.2"
   resolved "https://registry.yarnpkg.com/tenacious-fetch/-/tenacious-fetch-2.2.2.tgz#1d2cfdcb2eb270d2b5b47b5f0f04d76e6a203203"
@@ -8516,7 +8410,7 @@ yallist@^2.1.2:
   resolved "https://registry.yarnpkg.com/yallist/-/yallist-2.1.2.tgz#1c11f9218f076089a47dd512f93c6699a6a81d52"
   integrity sha1-HBH5IY8HYImkfdUS+TxmmaaoHVI=
 
-yallist@^3.0.0, yallist@^3.0.2, yallist@^3.0.3:
+yallist@^3.0.2:
   version "3.1.1"
   resolved "https://registry.yarnpkg.com/yallist/-/yallist-3.1.1.tgz#dbb7daf9bfd8bac9ab45ebf602b8cbad0d5d08fd"
   integrity sha512-a4UGQaWPH59mOXUYnAG2ewncQS4i4F43Tv3JoAM+s2VDAmS9NsK8GpDMLrCHPksFT7h3K6TOoUNn2pb7RoXx4g==