From 8951cf1acb926cc9b2cbc56e86d6ffb66111de52 Mon Sep 17 00:00:00 2001
From: arontommi <arontommi@gmail.com>
Date: Thu, 2 Apr 2020 08:59:01 +0200
Subject: [PATCH] .idea removed

---
 .idea/BamSegmegments.iml                      |  11 -
 .idea/markdown-navigator.xml                  |  71 ----
 .../markdown-navigator/profiles_settings.xml  |   3 -
 .idea/misc.xml                                |  14 -
 .idea/modules.xml                             |   8 -
 .idea/workspace.xml                           | 390 ------------------
 6 files changed, 497 deletions(-)
 delete mode 100644 .idea/BamSegmegments.iml
 delete mode 100644 .idea/markdown-navigator.xml
 delete mode 100644 .idea/markdown-navigator/profiles_settings.xml
 delete mode 100644 .idea/misc.xml
 delete mode 100644 .idea/modules.xml
 delete mode 100644 .idea/workspace.xml

diff --git a/.idea/BamSegmegments.iml b/.idea/BamSegmegments.iml
deleted file mode 100644
index 6711606..0000000
--- a/.idea/BamSegmegments.iml
+++ /dev/null
@@ -1,11 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<module type="PYTHON_MODULE" version="4">
-  <component name="NewModuleRootManager">
-    <content url="file://$MODULE_DIR$" />
-    <orderEntry type="inheritedJdk" />
-    <orderEntry type="sourceFolder" forTests="false" />
-  </component>
-  <component name="TestRunnerService">
-    <option name="PROJECT_TEST_RUNNER" value="Unittests" />
-  </component>
-</module>
\ No newline at end of file
diff --git a/.idea/markdown-navigator.xml b/.idea/markdown-navigator.xml
deleted file mode 100644
index 3efe9d6..0000000
--- a/.idea/markdown-navigator.xml
+++ /dev/null
@@ -1,71 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<project version="4">
-  <component name="MarkdownProjectSettings">
-    <PreviewSettings splitEditorLayout="SPLIT" splitEditorPreview="PREVIEW" useGrayscaleRendering="false" zoomFactor="1.0" maxImageWidth="0" showGitHubPageIfSynced="false" allowBrowsingInPreview="false" synchronizePreviewPosition="true" highlightPreviewType="NONE" highlightFadeOut="5" highlightOnTyping="true" synchronizeSourcePosition="true" verticallyAlignSourceAndPreviewSyncPosition="true" showSearchHighlightsInPreview="false" showSelectionInPreview="true">
-      <PanelProvider>
-        <provider providerId="com.vladsch.idea.multimarkdown.editor.swing.html.panel" providerName="Default - Swing" />
-      </PanelProvider>
-    </PreviewSettings>
-    <ParserSettings gitHubSyntaxChange="false">
-      <PegdownExtensions>
-        <option name="ABBREVIATIONS" value="false" />
-        <option name="ANCHORLINKS" value="true" />
-        <option name="ASIDE" value="false" />
-        <option name="ATXHEADERSPACE" value="true" />
-        <option name="AUTOLINKS" value="true" />
-        <option name="DEFINITIONS" value="false" />
-        <option name="DEFINITION_BREAK_DOUBLE_BLANK_LINE" value="false" />
-        <option name="FENCED_CODE_BLOCKS" value="true" />
-        <option name="FOOTNOTES" value="false" />
-        <option name="HARDWRAPS" value="false" />
-        <option name="INSERTED" value="false" />
-        <option name="QUOTES" value="false" />
-        <option name="RELAXEDHRULES" value="true" />
-        <option name="SMARTS" value="false" />
-        <option name="STRIKETHROUGH" value="true" />
-        <option name="SUBSCRIPT" value="false" />
-        <option name="SUPERSCRIPT" value="false" />
-        <option name="SUPPRESS_HTML_BLOCKS" value="false" />
-        <option name="SUPPRESS_INLINE_HTML" value="false" />
-        <option name="TABLES" value="true" />
-        <option name="TASKLISTITEMS" value="true" />
-        <option name="TOC" value="false" />
-        <option name="WIKILINKS" value="true" />
-      </PegdownExtensions>
-      <ParserOptions>
-        <option name="COMMONMARK_LISTS" value="true" />
-        <option name="DUMMY" value="false" />
-        <option name="EMOJI_SHORTCUTS" value="true" />
-        <option name="FLEXMARK_FRONT_MATTER" value="false" />
-        <option name="GFM_LOOSE_BLANK_LINE_AFTER_ITEM_PARA" value="false" />
-        <option name="GFM_TABLE_RENDERING" value="true" />
-        <option name="GITBOOK_URL_ENCODING" value="false" />
-        <option name="GITHUB_EMOJI_URL" value="false" />
-        <option name="GITHUB_LISTS" value="false" />
-        <option name="GITHUB_WIKI_LINKS" value="true" />
-        <option name="JEKYLL_FRONT_MATTER" value="false" />
-        <option name="SIM_TOC_BLANK_LINE_SPACER" value="true" />
-      </ParserOptions>
-    </ParserSettings>
-    <HtmlSettings headerTopEnabled="false" headerBottomEnabled="false" bodyTopEnabled="false" bodyBottomEnabled="false" embedUrlContent="false" addPageHeader="true">
-      <GeneratorProvider>
-        <provider providerId="com.vladsch.idea.multimarkdown.editor.swing.html.generator" providerName="Default Swing HTML Generator" />
-      </GeneratorProvider>
-      <headerTop />
-      <headerBottom />
-      <bodyTop />
-      <bodyBottom />
-    </HtmlSettings>
-    <CssSettings previewScheme="UI_SCHEME" cssUri="" isCssUriEnabled="false" isCssTextEnabled="false" isDynamicPageWidth="true">
-      <StylesheetProvider>
-        <provider providerId="com.vladsch.idea.multimarkdown.editor.swing.html.css" providerName="Default Swing Stylesheet" />
-      </StylesheetProvider>
-      <ScriptProviders />
-      <cssText />
-    </CssSettings>
-    <HtmlExportSettings updateOnSave="false" parentDir="$ProjectFileDir$" targetDir="$ProjectFileDir$" cssDir="" scriptDir="" plainHtml="false" imageDir="" copyLinkedImages="false" imageUniquifyType="0" targetExt="" useTargetExt="false" noCssNoScripts="false" linkToExportedHtml="true" exportOnSettingsChange="true" regenerateOnProjectOpen="false" />
-    <LinkMapSettings>
-      <textMaps />
-    </LinkMapSettings>
-  </component>
-</project>
\ No newline at end of file
diff --git a/.idea/markdown-navigator/profiles_settings.xml b/.idea/markdown-navigator/profiles_settings.xml
deleted file mode 100644
index 57927c5..0000000
--- a/.idea/markdown-navigator/profiles_settings.xml
+++ /dev/null
@@ -1,3 +0,0 @@
-<component name="MarkdownNavigator.ProfileManager">
-  <settings default="" pdf-export="" />
-</component>
\ No newline at end of file
diff --git a/.idea/misc.xml b/.idea/misc.xml
deleted file mode 100644
index 472bec8..0000000
--- a/.idea/misc.xml
+++ /dev/null
@@ -1,14 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<project version="4">
-  <component name="ProjectLevelVcsManager" settingsEditedManually="false">
-    <OptionsSetting value="true" id="Add" />
-    <OptionsSetting value="true" id="Remove" />
-    <OptionsSetting value="true" id="Checkout" />
-    <OptionsSetting value="true" id="Update" />
-    <OptionsSetting value="true" id="Status" />
-    <OptionsSetting value="true" id="Edit" />
-    <ConfirmationsSetting value="0" id="Add" />
-    <ConfirmationsSetting value="0" id="Remove" />
-  </component>
-  <component name="ProjectRootManager" version="2" project-jdk-name="Python 3.5.1 (/usr/local/Cellar/python3/3.5.1/Frameworks/Python.framework/Versions/3.5/bin/python3.5)" project-jdk-type="Python SDK" />
-</project>
\ No newline at end of file
diff --git a/.idea/modules.xml b/.idea/modules.xml
deleted file mode 100644
index 4bbaca5..0000000
--- a/.idea/modules.xml
+++ /dev/null
@@ -1,8 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<project version="4">
-  <component name="ProjectModuleManager">
-    <modules>
-      <module fileurl="file://$PROJECT_DIR$/.idea/BamSegmegments.iml" filepath="$PROJECT_DIR$/.idea/BamSegmegments.iml" />
-    </modules>
-  </component>
-</project>
\ No newline at end of file
diff --git a/.idea/workspace.xml b/.idea/workspace.xml
deleted file mode 100644
index 7f309dc..0000000
--- a/.idea/workspace.xml
+++ /dev/null
@@ -1,390 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<project version="4">
-  <component name="ChangeListManager">
-    <list default="true" id="3c0356ab-8810-48f6-990c-792d258b21de" name="Default" comment="" />
-    <ignored path="BamSegmegments.iws" />
-    <ignored path=".idea/workspace.xml" />
-    <option name="EXCLUDED_CONVERTED_TO_IGNORED" value="true" />
-    <option name="TRACKING_ENABLED" value="true" />
-    <option name="SHOW_DIALOG" value="false" />
-    <option name="HIGHLIGHT_CONFLICTS" value="true" />
-    <option name="HIGHLIGHT_NON_ACTIVE_CHANGELIST" value="false" />
-    <option name="LAST_RESOLUTION" value="IGNORE" />
-  </component>
-  <component name="CreatePatchCommitExecutor">
-    <option name="PATCH_PATH" value="" />
-  </component>
-  <component name="ExecutionTargetManager" SELECTED_TARGET="default_target" />
-  <component name="FavoritesManager">
-    <favorites_list name="BamSegmegments" />
-  </component>
-  <component name="FileEditorManager">
-    <leaf>
-      <file leaf-file-name="samtools_view.sh" pinned="false" current-in-tab="false">
-        <entry file="file://$PROJECT_DIR$/smallerbams/samtools_view.sh">
-          <provider selected="true" editor-type-id="text-editor">
-            <state relative-caret-position="90">
-              <caret line="6" column="27" selection-start-line="6" selection-start-column="27" selection-end-line="6" selection-end-column="27" />
-              <folding />
-            </state>
-          </provider>
-        </entry>
-      </file>
-      <file leaf-file-name="smallerbam.py" pinned="false" current-in-tab="false">
-        <entry file="file://$PROJECT_DIR$/smallerbams/smallerbam.py">
-          <provider selected="true" editor-type-id="text-editor">
-            <state relative-caret-position="654">
-              <caret line="51" column="27" selection-start-line="51" selection-start-column="27" selection-end-line="51" selection-end-column="27" />
-              <folding>
-                <element signature="e#0#23#0" expanded="true" />
-              </folding>
-            </state>
-          </provider>
-        </entry>
-      </file>
-      <file leaf-file-name="Readme.md" pinned="false" current-in-tab="true">
-        <entry file="file://$PROJECT_DIR$/Readme.md">
-          <provider selected="true" editor-type-id="split-provider[text-editor;MarkdownPreviewEditor]">
-            <state split_layout="SPLIT">
-              <first_editor relative-caret-position="225">
-                <caret line="15" column="77" selection-start-line="15" selection-start-column="77" selection-end-line="15" selection-end-column="77" />
-                <folding />
-              </first_editor>
-              <second_editor>
-                <js_state />
-              </second_editor>
-            </state>
-          </provider>
-        </entry>
-      </file>
-    </leaf>
-  </component>
-  <component name="FileTemplateManagerImpl">
-    <option name="RECENT_TEMPLATES">
-      <list>
-        <option value="Python Script" />
-      </list>
-    </option>
-  </component>
-  <component name="IdeDocumentHistory">
-    <option name="CHANGED_PATHS">
-      <list>
-        <option value="$PROJECT_DIR$/samtools_view.sh" />
-        <option value="$PROJECT_DIR$/smallerbam.py" />
-        <option value="$PROJECT_DIR$/smallerbams/samtools_view.sh" />
-        <option value="$PROJECT_DIR$/smallerbams/smallerbam.py" />
-        <option value="$PROJECT_DIR$/Readme.md" />
-      </list>
-    </option>
-  </component>
-  <component name="ProjectFrameBounds">
-    <option name="x" value="-2532" />
-    <option name="y" value="34" />
-    <option name="width" value="2185" />
-    <option name="height" value="1267" />
-  </component>
-  <component name="ProjectLevelVcsManager" settingsEditedManually="false">
-    <OptionsSetting value="true" id="Add" />
-    <OptionsSetting value="true" id="Remove" />
-    <OptionsSetting value="true" id="Checkout" />
-    <OptionsSetting value="true" id="Update" />
-    <OptionsSetting value="true" id="Status" />
-    <OptionsSetting value="true" id="Edit" />
-    <ConfirmationsSetting value="0" id="Add" />
-    <ConfirmationsSetting value="0" id="Remove" />
-  </component>
-  <component name="ProjectView">
-    <navigator currentView="ProjectPane" proportions="" version="1">
-      <flattenPackages />
-      <showMembers />
-      <showModules />
-      <showLibraryContents />
-      <hideEmptyPackages />
-      <abbreviatePackageNames />
-      <autoscrollToSource />
-      <autoscrollFromSource />
-      <sortByType />
-      <manualOrder />
-      <foldersAlwaysOnTop value="true" />
-    </navigator>
-    <panes>
-      <pane id="Scratches" />
-      <pane id="Scope" />
-      <pane id="ProjectPane">
-        <subPane>
-          <PATH>
-            <PATH_ELEMENT>
-              <option name="myItemId" value="BamSegmegments" />
-              <option name="myItemType" value="com.intellij.ide.projectView.impl.nodes.ProjectViewProjectNode" />
-            </PATH_ELEMENT>
-          </PATH>
-          <PATH>
-            <PATH_ELEMENT>
-              <option name="myItemId" value="BamSegmegments" />
-              <option name="myItemType" value="com.intellij.ide.projectView.impl.nodes.ProjectViewProjectNode" />
-            </PATH_ELEMENT>
-            <PATH_ELEMENT>
-              <option name="myItemId" value="BamSegmegments" />
-              <option name="myItemType" value="com.intellij.ide.projectView.impl.nodes.PsiDirectoryNode" />
-            </PATH_ELEMENT>
-          </PATH>
-          <PATH>
-            <PATH_ELEMENT>
-              <option name="myItemId" value="BamSegmegments" />
-              <option name="myItemType" value="com.intellij.ide.projectView.impl.nodes.ProjectViewProjectNode" />
-            </PATH_ELEMENT>
-            <PATH_ELEMENT>
-              <option name="myItemId" value="BamSegmegments" />
-              <option name="myItemType" value="com.intellij.ide.projectView.impl.nodes.PsiDirectoryNode" />
-            </PATH_ELEMENT>
-            <PATH_ELEMENT>
-              <option name="myItemId" value="smallerbams" />
-              <option name="myItemType" value="com.intellij.ide.projectView.impl.nodes.PsiDirectoryNode" />
-            </PATH_ELEMENT>
-          </PATH>
-        </subPane>
-      </pane>
-    </panes>
-  </component>
-  <component name="RecentsManager">
-    <key name="MoveFile.RECENT_KEYS">
-      <recent name="$PROJECT_DIR$/smallerbams" />
-    </key>
-  </component>
-  <component name="RunManager">
-    <configuration default="true" type="BashConfigurationType" factoryName="Bash">
-      <option name="INTERPRETER_OPTIONS" value="" />
-      <option name="INTERPRETER_PATH" value="/bin/bash" />
-      <option name="WORKING_DIRECTORY" value="" />
-      <option name="PARENT_ENVS" value="true" />
-      <option name="SCRIPT_NAME" value="" />
-      <option name="PARAMETERS" value="" />
-      <module name="" />
-      <envs />
-      <method />
-    </configuration>
-    <configuration default="true" type="PythonConfigurationType" factoryName="Python">
-      <option name="INTERPRETER_OPTIONS" value="" />
-      <option name="PARENT_ENVS" value="true" />
-      <envs>
-        <env name="PYTHONUNBUFFERED" value="1" />
-      </envs>
-      <option name="SDK_HOME" value="" />
-      <option name="WORKING_DIRECTORY" value="" />
-      <option name="IS_MODULE_SDK" value="false" />
-      <option name="ADD_CONTENT_ROOTS" value="true" />
-      <option name="ADD_SOURCE_ROOTS" value="true" />
-      <module name="BamSegmegments" />
-      <option name="SCRIPT_NAME" value="" />
-      <option name="PARAMETERS" value="" />
-      <option name="SHOW_COMMAND_LINE" value="false" />
-      <method />
-    </configuration>
-    <configuration default="true" type="Tox" factoryName="Tox">
-      <option name="INTERPRETER_OPTIONS" value="" />
-      <option name="PARENT_ENVS" value="true" />
-      <envs />
-      <option name="SDK_HOME" value="" />
-      <option name="WORKING_DIRECTORY" value="" />
-      <option name="IS_MODULE_SDK" value="false" />
-      <option name="ADD_CONTENT_ROOTS" value="true" />
-      <option name="ADD_SOURCE_ROOTS" value="true" />
-      <module name="BamSegmegments" />
-      <method />
-    </configuration>
-    <configuration default="true" type="tests" factoryName="Attests">
-      <option name="INTERPRETER_OPTIONS" value="" />
-      <option name="PARENT_ENVS" value="true" />
-      <envs />
-      <option name="SDK_HOME" value="" />
-      <option name="WORKING_DIRECTORY" value="" />
-      <option name="IS_MODULE_SDK" value="false" />
-      <option name="ADD_CONTENT_ROOTS" value="true" />
-      <option name="ADD_SOURCE_ROOTS" value="true" />
-      <module name="BamSegmegments" />
-      <option name="SCRIPT_NAME" value="" />
-      <option name="CLASS_NAME" value="" />
-      <option name="METHOD_NAME" value="" />
-      <option name="FOLDER_NAME" value="" />
-      <option name="TEST_TYPE" value="TEST_SCRIPT" />
-      <option name="PATTERN" value="" />
-      <option name="USE_PATTERN" value="false" />
-      <method />
-    </configuration>
-    <configuration default="true" type="tests" factoryName="Doctests">
-      <option name="INTERPRETER_OPTIONS" value="" />
-      <option name="PARENT_ENVS" value="true" />
-      <envs />
-      <option name="SDK_HOME" value="" />
-      <option name="WORKING_DIRECTORY" value="" />
-      <option name="IS_MODULE_SDK" value="false" />
-      <option name="ADD_CONTENT_ROOTS" value="true" />
-      <option name="ADD_SOURCE_ROOTS" value="true" />
-      <module name="BamSegmegments" />
-      <option name="SCRIPT_NAME" value="" />
-      <option name="CLASS_NAME" value="" />
-      <option name="METHOD_NAME" value="" />
-      <option name="FOLDER_NAME" value="" />
-      <option name="TEST_TYPE" value="TEST_SCRIPT" />
-      <option name="PATTERN" value="" />
-      <option name="USE_PATTERN" value="false" />
-      <method />
-    </configuration>
-    <configuration default="true" type="tests" factoryName="Nosetests">
-      <option name="INTERPRETER_OPTIONS" value="" />
-      <option name="PARENT_ENVS" value="true" />
-      <envs />
-      <option name="SDK_HOME" value="" />
-      <option name="WORKING_DIRECTORY" value="" />
-      <option name="IS_MODULE_SDK" value="false" />
-      <option name="ADD_CONTENT_ROOTS" value="true" />
-      <option name="ADD_SOURCE_ROOTS" value="true" />
-      <module name="BamSegmegments" />
-      <option name="SCRIPT_NAME" value="" />
-      <option name="CLASS_NAME" value="" />
-      <option name="METHOD_NAME" value="" />
-      <option name="FOLDER_NAME" value="" />
-      <option name="TEST_TYPE" value="TEST_SCRIPT" />
-      <option name="PATTERN" value="" />
-      <option name="USE_PATTERN" value="false" />
-      <option name="PARAMS" value="" />
-      <option name="USE_PARAM" value="false" />
-      <method />
-    </configuration>
-    <configuration default="true" type="tests" factoryName="Unittests">
-      <option name="INTERPRETER_OPTIONS" value="" />
-      <option name="PARENT_ENVS" value="true" />
-      <envs />
-      <option name="SDK_HOME" value="" />
-      <option name="WORKING_DIRECTORY" value="" />
-      <option name="IS_MODULE_SDK" value="false" />
-      <option name="ADD_CONTENT_ROOTS" value="true" />
-      <option name="ADD_SOURCE_ROOTS" value="true" />
-      <module name="BamSegmegments" />
-      <option name="SCRIPT_NAME" value="" />
-      <option name="CLASS_NAME" value="" />
-      <option name="METHOD_NAME" value="" />
-      <option name="FOLDER_NAME" value="" />
-      <option name="TEST_TYPE" value="TEST_SCRIPT" />
-      <option name="PATTERN" value="" />
-      <option name="USE_PATTERN" value="false" />
-      <option name="PUREUNITTEST" value="true" />
-      <option name="PARAMS" value="" />
-      <option name="USE_PARAM" value="false" />
-      <method />
-    </configuration>
-    <configuration default="true" type="tests" factoryName="py.test">
-      <option name="INTERPRETER_OPTIONS" value="" />
-      <option name="PARENT_ENVS" value="true" />
-      <envs />
-      <option name="SDK_HOME" value="" />
-      <option name="WORKING_DIRECTORY" value="" />
-      <option name="IS_MODULE_SDK" value="false" />
-      <option name="ADD_CONTENT_ROOTS" value="true" />
-      <option name="ADD_SOURCE_ROOTS" value="true" />
-      <module name="BamSegmegments" />
-      <option name="SCRIPT_NAME" value="" />
-      <option name="CLASS_NAME" value="" />
-      <option name="METHOD_NAME" value="" />
-      <option name="FOLDER_NAME" value="" />
-      <option name="TEST_TYPE" value="TEST_SCRIPT" />
-      <option name="PATTERN" value="" />
-      <option name="USE_PATTERN" value="false" />
-      <option name="testToRun" value="" />
-      <option name="keywords" value="" />
-      <option name="params" value="" />
-      <option name="USE_PARAM" value="false" />
-      <option name="USE_KEYWORD" value="false" />
-      <method />
-    </configuration>
-  </component>
-  <component name="ShelveChangesManager" show_recycled="false">
-    <option name="remove_strategy" value="false" />
-  </component>
-  <component name="SvnConfiguration">
-    <configuration />
-  </component>
-  <component name="TaskManager">
-    <task active="true" id="Default" summary="Default task">
-      <changelist id="3c0356ab-8810-48f6-990c-792d258b21de" name="Default" comment="" />
-      <created>1515661531113</created>
-      <option name="number" value="Default" />
-      <option name="presentableId" value="Default" />
-      <updated>1515661531113</updated>
-    </task>
-    <servers />
-  </component>
-  <component name="ToolWindowManager">
-    <frame x="-2532" y="34" width="2185" height="1267" extended-state="0" />
-    <editor active="true" />
-    <layout>
-      <window_info id="Project" active="false" anchor="left" auto_hide="false" internal_type="DOCKED" type="DOCKED" visible="true" show_stripe_button="true" weight="0.14510167" sideWeight="0.5" order="0" side_tool="false" content_ui="combo" />
-      <window_info id="TODO" active="false" anchor="bottom" auto_hide="false" internal_type="DOCKED" type="DOCKED" visible="false" show_stripe_button="true" weight="0.33" sideWeight="0.5" order="6" side_tool="false" content_ui="tabs" />
-      <window_info id="Event Log" active="false" anchor="bottom" auto_hide="false" internal_type="DOCKED" type="DOCKED" visible="false" show_stripe_button="true" weight="0.33" sideWeight="0.5" order="-1" side_tool="true" content_ui="tabs" />
-      <window_info id="Version Control" active="false" anchor="bottom" auto_hide="false" internal_type="DOCKED" type="DOCKED" visible="false" show_stripe_button="true" weight="0.33" sideWeight="0.5" order="-1" side_tool="false" content_ui="tabs" />
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