@jbrowse/plugin-alignments 2.2.0 → 2.2.1

package/src/AlignmentsFeatureDetail/__snapshots__/index.test.js.snap

@@ -73,9 +73,7 @@ exports[`open up a widget 1`] = `
                 <div
                   class="css-1omt041-fieldValue"
                 >
-                  <div>
-                    ctgA:3..102 (+)
-                  </div>
+                  ctgA:3..102 (+)
                 </div>
               </div>
               <div
@@ -325,475 +323,5 @@ exports[`open up a widget 1`] = `
       </div>
     </div>
   </div>
-  <div
-    class="MuiPaper-root MuiPaper-elevation MuiPaper-rounded MuiPaper-elevation1 MuiAccordion-root MuiAccordion-rounded Mui-expanded MuiAccordion-gutters css-1elwnq4-MuiPaper-root-MuiAccordion-root"
-  >
-    <div
-      aria-expanded="true"
-      class="MuiButtonBase-root MuiAccordionSummary-root Mui-expanded MuiAccordionSummary-gutters css-sh22l5-MuiButtonBase-root-MuiAccordionSummary-root"
-      role="button"
-      tabindex="0"
-    >
-      <div
-        class="MuiAccordionSummary-content Mui-expanded MuiAccordionSummary-contentGutters css-o4b71y-MuiAccordionSummary-content"
-      >
-        <span
-          class="MuiTypography-root MuiTypography-button css-1f0on15-MuiTypography-root"
-        >
-           
-          Flags
-        </span>
-      </div>
-      <div
-        class="MuiAccordionSummary-expandIconWrapper Mui-expanded css-yw020d-MuiAccordionSummary-expandIconWrapper"
-      >
-        <svg
-          aria-hidden="true"
-          class="MuiSvgIcon-root MuiSvgIcon-fontSizeMedium css-125qixp-MuiSvgIcon-root-expandIcon"
-          data-testid="ExpandMoreIcon"
-          focusable="false"
-          viewBox="0 0 24 24"
-        >
-          <path
-            d="M16.59 8.59 12 13.17 7.41 8.59 6 10l6 6 6-6z"
-          />
-        </svg>
-      </div>
-    </div>
-    <div
-      class="MuiCollapse-root MuiCollapse-vertical MuiCollapse-entered css-pwcg7p-MuiCollapse-root"
-      style="min-height: 0px;"
-    >
-      <div
-        class="MuiCollapse-wrapper MuiCollapse-vertical css-smkl36-MuiCollapse-wrapper"
-      >
-        <div
-          class="MuiCollapse-wrapperInner MuiCollapse-vertical css-9l5vo-MuiCollapse-wrapperInner"
-        >
-          <div
-            class="MuiAccordion-region"
-            role="region"
-          >
-            <div
-              class="MuiAccordionDetails-root css-rqrb7m-MuiAccordionDetails-root-expansionPanelDetails"
-            >
-              <div
-                class="MuiFormGroup-root css-dmmspl-MuiFormGroup-root"
-              >
-                <label
-                  class="MuiFormControlLabel-root MuiFormControlLabel-labelPlacementEnd css-j204z7-MuiFormControlLabel-root"
-                >
-                  <span
-                    class="MuiButtonBase-root MuiCheckbox-root MuiCheckbox-colorPrimary PrivateSwitchBase-root MuiCheckbox-root MuiCheckbox-colorPrimary MuiCheckbox-root MuiCheckbox-colorPrimary css-1r7hq7f-MuiButtonBase-root-MuiCheckbox-root-compact"
-                  >
-                    <input
-                      class="PrivateSwitchBase-input css-1m9pwf3"
-                      data-indeterminate="false"
-                      name="read paired"
-                      readonly=""
-                      type="checkbox"
-                    />
-                    <svg
-                      aria-hidden="true"
-                      class="MuiSvgIcon-root MuiSvgIcon-fontSizeMedium css-i4bv87-MuiSvgIcon-root"
-                      data-testid="CheckBoxOutlineBlankIcon"
-                      focusable="false"
-                      viewBox="0 0 24 24"
-                    >
-                      <path
-                        d="M19 5v14H5V5h14m0-2H5c-1.1 0-2 .9-2 2v14c0 1.1.9 2 2 2h14c1.1 0 2-.9 2-2V5c0-1.1-.9-2-2-2z"
-                      />
-                    </svg>
-                    <span
-                      class="MuiTouchRipple-root css-8je8zh-MuiTouchRipple-root"
-                    />
-                  </span>
-                  <span
-                    class="MuiTypography-root MuiTypography-body1 MuiFormControlLabel-label css-ahj2mt-MuiTypography-root"
-                  >
-                    read paired
-                  </span>
-                </label>
-                <label
-                  class="MuiFormControlLabel-root MuiFormControlLabel-labelPlacementEnd css-j204z7-MuiFormControlLabel-root"
-                >
-                  <span
-                    class="MuiButtonBase-root MuiCheckbox-root MuiCheckbox-colorPrimary PrivateSwitchBase-root MuiCheckbox-root MuiCheckbox-colorPrimary MuiCheckbox-root MuiCheckbox-colorPrimary css-1r7hq7f-MuiButtonBase-root-MuiCheckbox-root-compact"
-                  >
-                    <input
-                      class="PrivateSwitchBase-input css-1m9pwf3"
-                      data-indeterminate="false"
-                      name="read mapped in proper pair"
-                      readonly=""
-                      type="checkbox"
-                    />
-                    <svg
-                      aria-hidden="true"
-                      class="MuiSvgIcon-root MuiSvgIcon-fontSizeMedium css-i4bv87-MuiSvgIcon-root"
-                      data-testid="CheckBoxOutlineBlankIcon"
-                      focusable="false"
-                      viewBox="0 0 24 24"
-                    >
-                      <path
-                        d="M19 5v14H5V5h14m0-2H5c-1.1 0-2 .9-2 2v14c0 1.1.9 2 2 2h14c1.1 0 2-.9 2-2V5c0-1.1-.9-2-2-2z"
-                      />
-                    </svg>
-                    <span
-                      class="MuiTouchRipple-root css-8je8zh-MuiTouchRipple-root"
-                    />
-                  </span>
-                  <span
-                    class="MuiTypography-root MuiTypography-body1 MuiFormControlLabel-label css-ahj2mt-MuiTypography-root"
-                  >
-                    read mapped in proper pair
-                  </span>
-                </label>
-                <label
-                  class="MuiFormControlLabel-root MuiFormControlLabel-labelPlacementEnd css-j204z7-MuiFormControlLabel-root"
-                >
-                  <span
-                    class="MuiButtonBase-root MuiCheckbox-root MuiCheckbox-colorPrimary PrivateSwitchBase-root MuiCheckbox-root MuiCheckbox-colorPrimary MuiCheckbox-root MuiCheckbox-colorPrimary css-1r7hq7f-MuiButtonBase-root-MuiCheckbox-root-compact"
-                  >
-                    <input
-                      class="PrivateSwitchBase-input css-1m9pwf3"
-                      data-indeterminate="false"
-                      name="read unmapped"
-                      readonly=""
-                      type="checkbox"
-                    />
-                    <svg
-                      aria-hidden="true"
-                      class="MuiSvgIcon-root MuiSvgIcon-fontSizeMedium css-i4bv87-MuiSvgIcon-root"
-                      data-testid="CheckBoxOutlineBlankIcon"
-                      focusable="false"
-                      viewBox="0 0 24 24"
-                    >
-                      <path
-                        d="M19 5v14H5V5h14m0-2H5c-1.1 0-2 .9-2 2v14c0 1.1.9 2 2 2h14c1.1 0 2-.9 2-2V5c0-1.1-.9-2-2-2z"
-                      />
-                    </svg>
-                    <span
-                      class="MuiTouchRipple-root css-8je8zh-MuiTouchRipple-root"
-                    />
-                  </span>
-                  <span
-                    class="MuiTypography-root MuiTypography-body1 MuiFormControlLabel-label css-ahj2mt-MuiTypography-root"
-                  >
-                    read unmapped
-                  </span>
-                </label>
-                <label
-                  class="MuiFormControlLabel-root MuiFormControlLabel-labelPlacementEnd css-j204z7-MuiFormControlLabel-root"
-                >
-                  <span
-                    class="MuiButtonBase-root MuiCheckbox-root MuiCheckbox-colorPrimary PrivateSwitchBase-root MuiCheckbox-root MuiCheckbox-colorPrimary MuiCheckbox-root MuiCheckbox-colorPrimary css-1r7hq7f-MuiButtonBase-root-MuiCheckbox-root-compact"
-                  >
-                    <input
-                      class="PrivateSwitchBase-input css-1m9pwf3"
-                      data-indeterminate="false"
-                      name="mate unmapped"
-                      readonly=""
-                      type="checkbox"
-                    />
-                    <svg
-                      aria-hidden="true"
-                      class="MuiSvgIcon-root MuiSvgIcon-fontSizeMedium css-i4bv87-MuiSvgIcon-root"
-                      data-testid="CheckBoxOutlineBlankIcon"
-                      focusable="false"
-                      viewBox="0 0 24 24"
-                    >
-                      <path
-                        d="M19 5v14H5V5h14m0-2H5c-1.1 0-2 .9-2 2v14c0 1.1.9 2 2 2h14c1.1 0 2-.9 2-2V5c0-1.1-.9-2-2-2z"
-                      />
-                    </svg>
-                    <span
-                      class="MuiTouchRipple-root css-8je8zh-MuiTouchRipple-root"
-                    />
-                  </span>
-                  <span
-                    class="MuiTypography-root MuiTypography-body1 MuiFormControlLabel-label css-ahj2mt-MuiTypography-root"
-                  >
-                    mate unmapped
-                  </span>
-                </label>
-                <label
-                  class="MuiFormControlLabel-root MuiFormControlLabel-labelPlacementEnd css-j204z7-MuiFormControlLabel-root"
-                >
-                  <span
-                    class="MuiButtonBase-root MuiCheckbox-root MuiCheckbox-colorPrimary PrivateSwitchBase-root MuiCheckbox-root MuiCheckbox-colorPrimary MuiCheckbox-root MuiCheckbox-colorPrimary css-1r7hq7f-MuiButtonBase-root-MuiCheckbox-root-compact"
-                  >
-                    <input
-                      class="PrivateSwitchBase-input css-1m9pwf3"
-                      data-indeterminate="false"
-                      name="read reverse strand"
-                      readonly=""
-                      type="checkbox"
-                    />
-                    <svg
-                      aria-hidden="true"
-                      class="MuiSvgIcon-root MuiSvgIcon-fontSizeMedium css-i4bv87-MuiSvgIcon-root"
-                      data-testid="CheckBoxOutlineBlankIcon"
-                      focusable="false"
-                      viewBox="0 0 24 24"
-                    >
-                      <path
-                        d="M19 5v14H5V5h14m0-2H5c-1.1 0-2 .9-2 2v14c0 1.1.9 2 2 2h14c1.1 0 2-.9 2-2V5c0-1.1-.9-2-2-2z"
-                      />
-                    </svg>
-                    <span
-                      class="MuiTouchRipple-root css-8je8zh-MuiTouchRipple-root"
-                    />
-                  </span>
-                  <span
-                    class="MuiTypography-root MuiTypography-body1 MuiFormControlLabel-label css-ahj2mt-MuiTypography-root"
-                  >
-                    read reverse strand
-                  </span>
-                </label>
-                <label
-                  class="MuiFormControlLabel-root MuiFormControlLabel-labelPlacementEnd css-j204z7-MuiFormControlLabel-root"
-                >
-                  <span
-                    class="MuiButtonBase-root MuiCheckbox-root MuiCheckbox-colorPrimary PrivateSwitchBase-root MuiCheckbox-root MuiCheckbox-colorPrimary MuiCheckbox-root MuiCheckbox-colorPrimary css-1r7hq7f-MuiButtonBase-root-MuiCheckbox-root-compact"
-                  >
-                    <input
-                      class="PrivateSwitchBase-input css-1m9pwf3"
-                      data-indeterminate="false"
-                      name="mate reverse strand"
-                      readonly=""
-                      type="checkbox"
-                    />
-                    <svg
-                      aria-hidden="true"
-                      class="MuiSvgIcon-root MuiSvgIcon-fontSizeMedium css-i4bv87-MuiSvgIcon-root"
-                      data-testid="CheckBoxOutlineBlankIcon"
-                      focusable="false"
-                      viewBox="0 0 24 24"
-                    >
-                      <path
-                        d="M19 5v14H5V5h14m0-2H5c-1.1 0-2 .9-2 2v14c0 1.1.9 2 2 2h14c1.1 0 2-.9 2-2V5c0-1.1-.9-2-2-2z"
-                      />
-                    </svg>
-                    <span
-                      class="MuiTouchRipple-root css-8je8zh-MuiTouchRipple-root"
-                    />
-                  </span>
-                  <span
-                    class="MuiTypography-root MuiTypography-body1 MuiFormControlLabel-label css-ahj2mt-MuiTypography-root"
-                  >
-                    mate reverse strand
-                  </span>
-                </label>
-                <label
-                  class="MuiFormControlLabel-root MuiFormControlLabel-labelPlacementEnd css-j204z7-MuiFormControlLabel-root"
-                >
-                  <span
-                    class="MuiButtonBase-root MuiCheckbox-root MuiCheckbox-colorPrimary PrivateSwitchBase-root MuiCheckbox-root MuiCheckbox-colorPrimary MuiCheckbox-root MuiCheckbox-colorPrimary css-1r7hq7f-MuiButtonBase-root-MuiCheckbox-root-compact"
-                  >
-                    <input
-                      class="PrivateSwitchBase-input css-1m9pwf3"
-                      data-indeterminate="false"
-                      name="first in pair"
-                      readonly=""
-                      type="checkbox"
-                    />
-                    <svg
-                      aria-hidden="true"
-                      class="MuiSvgIcon-root MuiSvgIcon-fontSizeMedium css-i4bv87-MuiSvgIcon-root"
-                      data-testid="CheckBoxOutlineBlankIcon"
-                      focusable="false"
-                      viewBox="0 0 24 24"
-                    >
-                      <path
-                        d="M19 5v14H5V5h14m0-2H5c-1.1 0-2 .9-2 2v14c0 1.1.9 2 2 2h14c1.1 0 2-.9 2-2V5c0-1.1-.9-2-2-2z"
-                      />
-                    </svg>
-                    <span
-                      class="MuiTouchRipple-root css-8je8zh-MuiTouchRipple-root"
-                    />
-                  </span>
-                  <span
-                    class="MuiTypography-root MuiTypography-body1 MuiFormControlLabel-label css-ahj2mt-MuiTypography-root"
-                  >
-                    first in pair
-                  </span>
-                </label>
-                <label
-                  class="MuiFormControlLabel-root MuiFormControlLabel-labelPlacementEnd css-j204z7-MuiFormControlLabel-root"
-                >
-                  <span
-                    class="MuiButtonBase-root MuiCheckbox-root MuiCheckbox-colorPrimary PrivateSwitchBase-root MuiCheckbox-root MuiCheckbox-colorPrimary MuiCheckbox-root MuiCheckbox-colorPrimary css-1r7hq7f-MuiButtonBase-root-MuiCheckbox-root-compact"
-                  >
-                    <input
-                      class="PrivateSwitchBase-input css-1m9pwf3"
-                      data-indeterminate="false"
-                      name="second in pair"
-                      readonly=""
-                      type="checkbox"
-                    />
-                    <svg
-                      aria-hidden="true"
-                      class="MuiSvgIcon-root MuiSvgIcon-fontSizeMedium css-i4bv87-MuiSvgIcon-root"
-                      data-testid="CheckBoxOutlineBlankIcon"
-                      focusable="false"
-                      viewBox="0 0 24 24"
-                    >
-                      <path
-                        d="M19 5v14H5V5h14m0-2H5c-1.1 0-2 .9-2 2v14c0 1.1.9 2 2 2h14c1.1 0 2-.9 2-2V5c0-1.1-.9-2-2-2z"
-                      />
-                    </svg>
-                    <span
-                      class="MuiTouchRipple-root css-8je8zh-MuiTouchRipple-root"
-                    />
-                  </span>
-                  <span
-                    class="MuiTypography-root MuiTypography-body1 MuiFormControlLabel-label css-ahj2mt-MuiTypography-root"
-                  >
-                    second in pair
-                  </span>
-                </label>
-                <label
-                  class="MuiFormControlLabel-root MuiFormControlLabel-labelPlacementEnd css-j204z7-MuiFormControlLabel-root"
-                >
-                  <span
-                    class="MuiButtonBase-root MuiCheckbox-root MuiCheckbox-colorPrimary PrivateSwitchBase-root MuiCheckbox-root MuiCheckbox-colorPrimary MuiCheckbox-root MuiCheckbox-colorPrimary css-1r7hq7f-MuiButtonBase-root-MuiCheckbox-root-compact"
-                  >
-                    <input
-                      class="PrivateSwitchBase-input css-1m9pwf3"
-                      data-indeterminate="false"
-                      name="not primary alignment"
-                      readonly=""
-                      type="checkbox"
-                    />
-                    <svg
-                      aria-hidden="true"
-                      class="MuiSvgIcon-root MuiSvgIcon-fontSizeMedium css-i4bv87-MuiSvgIcon-root"
-                      data-testid="CheckBoxOutlineBlankIcon"
-                      focusable="false"
-                      viewBox="0 0 24 24"
-                    >
-                      <path
-                        d="M19 5v14H5V5h14m0-2H5c-1.1 0-2 .9-2 2v14c0 1.1.9 2 2 2h14c1.1 0 2-.9 2-2V5c0-1.1-.9-2-2-2z"
-                      />
-                    </svg>
-                    <span
-                      class="MuiTouchRipple-root css-8je8zh-MuiTouchRipple-root"
-                    />
-                  </span>
-                  <span
-                    class="MuiTypography-root MuiTypography-body1 MuiFormControlLabel-label css-ahj2mt-MuiTypography-root"
-                  >
-                    not primary alignment
-                  </span>
-                </label>
-                <label
-                  class="MuiFormControlLabel-root MuiFormControlLabel-labelPlacementEnd css-j204z7-MuiFormControlLabel-root"
-                >
-                  <span
-                    class="MuiButtonBase-root MuiCheckbox-root MuiCheckbox-colorPrimary PrivateSwitchBase-root MuiCheckbox-root MuiCheckbox-colorPrimary MuiCheckbox-root MuiCheckbox-colorPrimary css-1r7hq7f-MuiButtonBase-root-MuiCheckbox-root-compact"
-                  >
-                    <input
-                      class="PrivateSwitchBase-input css-1m9pwf3"
-                      data-indeterminate="false"
-                      name="read fails platform/vendor quality checks"
-                      readonly=""
-                      type="checkbox"
-                    />
-                    <svg
-                      aria-hidden="true"
-                      class="MuiSvgIcon-root MuiSvgIcon-fontSizeMedium css-i4bv87-MuiSvgIcon-root"
-                      data-testid="CheckBoxOutlineBlankIcon"
-                      focusable="false"
-                      viewBox="0 0 24 24"
-                    >
-                      <path
-                        d="M19 5v14H5V5h14m0-2H5c-1.1 0-2 .9-2 2v14c0 1.1.9 2 2 2h14c1.1 0 2-.9 2-2V5c0-1.1-.9-2-2-2z"
-                      />
-                    </svg>
-                    <span
-                      class="MuiTouchRipple-root css-8je8zh-MuiTouchRipple-root"
-                    />
-                  </span>
-                  <span
-                    class="MuiTypography-root MuiTypography-body1 MuiFormControlLabel-label css-ahj2mt-MuiTypography-root"
-                  >
-                    read fails platform/vendor quality checks
-                  </span>
-                </label>
-                <label
-                  class="MuiFormControlLabel-root MuiFormControlLabel-labelPlacementEnd css-j204z7-MuiFormControlLabel-root"
-                >
-                  <span
-                    class="MuiButtonBase-root MuiCheckbox-root MuiCheckbox-colorPrimary PrivateSwitchBase-root MuiCheckbox-root MuiCheckbox-colorPrimary MuiCheckbox-root MuiCheckbox-colorPrimary css-1r7hq7f-MuiButtonBase-root-MuiCheckbox-root-compact"
-                  >
-                    <input
-                      class="PrivateSwitchBase-input css-1m9pwf3"
-                      data-indeterminate="false"
-                      name="read is PCR or optical duplicate"
-                      readonly=""
-                      type="checkbox"
-                    />
-                    <svg
-                      aria-hidden="true"
-                      class="MuiSvgIcon-root MuiSvgIcon-fontSizeMedium css-i4bv87-MuiSvgIcon-root"
-                      data-testid="CheckBoxOutlineBlankIcon"
-                      focusable="false"
-                      viewBox="0 0 24 24"
-                    >
-                      <path
-                        d="M19 5v14H5V5h14m0-2H5c-1.1 0-2 .9-2 2v14c0 1.1.9 2 2 2h14c1.1 0 2-.9 2-2V5c0-1.1-.9-2-2-2z"
-                      />
-                    </svg>
-                    <span
-                      class="MuiTouchRipple-root css-8je8zh-MuiTouchRipple-root"
-                    />
-                  </span>
-                  <span
-                    class="MuiTypography-root MuiTypography-body1 MuiFormControlLabel-label css-ahj2mt-MuiTypography-root"
-                  >
-                    read is PCR or optical duplicate
-                  </span>
-                </label>
-                <label
-                  class="MuiFormControlLabel-root MuiFormControlLabel-labelPlacementEnd css-j204z7-MuiFormControlLabel-root"
-                >
-                  <span
-                    class="MuiButtonBase-root MuiCheckbox-root MuiCheckbox-colorPrimary PrivateSwitchBase-root MuiCheckbox-root MuiCheckbox-colorPrimary MuiCheckbox-root MuiCheckbox-colorPrimary css-1r7hq7f-MuiButtonBase-root-MuiCheckbox-root-compact"
-                  >
-                    <input
-                      class="PrivateSwitchBase-input css-1m9pwf3"
-                      data-indeterminate="false"
-                      name="supplementary alignment"
-                      readonly=""
-                      type="checkbox"
-                    />
-                    <svg
-                      aria-hidden="true"
-                      class="MuiSvgIcon-root MuiSvgIcon-fontSizeMedium css-i4bv87-MuiSvgIcon-root"
-                      data-testid="CheckBoxOutlineBlankIcon"
-                      focusable="false"
-                      viewBox="0 0 24 24"
-                    >
-                      <path
-                        d="M19 5v14H5V5h14m0-2H5c-1.1 0-2 .9-2 2v14c0 1.1.9 2 2 2h14c1.1 0 2-.9 2-2V5c0-1.1-.9-2-2-2z"
-                      />
-                    </svg>
-                    <span
-                      class="MuiTouchRipple-root css-8je8zh-MuiTouchRipple-root"
-                    />
-                  </span>
-                  <span
-                    class="MuiTypography-root MuiTypography-body1 MuiFormControlLabel-label css-ahj2mt-MuiTypography-root"
-                  >
-                    supplementary alignment
-                  </span>
-                </label>
-              </div>
-            </div>
-          </div>
-        </div>
-      </div>
-    </div>
-  </div>
 </div>
 `;

package/src/AlignmentsFeatureDetail/index.test.js

@@ -11,14 +11,16 @@ test('open up a widget', () => {
   const pluginManager = new PluginManager([])
 
   const Session = types.model({
-    pluginManager: types.optional(types.frozen(), {}),
     rpcManager: types.optional(types.frozen(), {}),
     configuration: ConfigurationSchema('test', {}),
     widget: stateModelFactory(pluginManager),
   })
-  const session = Session.create({
-    widget: { type: 'AlignmentsFeatureWidget' },
-  })
+  const session = Session.create(
+    {
+      widget: { type: 'AlignmentsFeatureWidget' },
+    },
+    { pluginManager },
+  )
   session.widget.setFeatureData({
     seq: 'TTGTTGCGGAGTTGAACAACGGCATTAGGAACACTTCCGTCTCTCACTTTTATACGATTATGATTGGTTCTTTAGCCTTGGTTTAGATTGGTAGTAGTAG',
     start: 2,

package/src/BamAdapter/BamAdapter.ts

@@ -4,11 +4,12 @@ import {
   BaseOptions,
 } from '@jbrowse/core/data_adapters/BaseAdapter'
 import { Region } from '@jbrowse/core/util/types'
-import { bytesForRegions, updateStatus } from '@jbrowse/core/util'
+import { bytesForRegions, updateStatus, Feature } from '@jbrowse/core/util'
 import { openLocation } from '@jbrowse/core/util/io'
 import { ObservableCreate } from '@jbrowse/core/util/rxjs'
-import { Feature } from '@jbrowse/core/util/simpleFeature'
 import { toArray } from 'rxjs/operators'
+
+// locals
 import BamSlightlyLazyFeature from './BamSlightlyLazyFeature'
 
 interface Header {

package/src/BamAdapter/BamSlightlyLazyFeature.ts

@@ -4,8 +4,9 @@ import {
   SimpleFeatureSerialized,
 } from '@jbrowse/core/util/simpleFeature'
 import { BamRecord } from '@gmod/bam'
-import { getMismatches } from './MismatchParser'
 
+// locals
+import { getMismatches } from './MismatchParser'
 import BamAdapter from './BamAdapter'
 
 export default class BamSlightlyLazyFeature implements Feature {

package/src/BamAdapter/MismatchParser.test.ts

@@ -139,79 +139,88 @@ test('more skip', () => {
       (a, b) => a.start - b.start,
     ),
   ).toMatchInlineSnapshot(`
-    Array [
-      Object {
+    [
+      {
         "altbase": "G",
         "base": "A",
         "length": 1,
+        "qual": undefined,
         "start": 6,
         "type": "mismatch",
       },
-      Object {
+      {
         "altbase": "C",
         "base": "A",
         "length": 1,
+        "qual": undefined,
         "start": 11,
         "type": "mismatch",
       },
-      Object {
+      {
         "base": "1",
         "length": 0,
         "start": 31,
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