Draft: Fix memory problem with alt hla

.claude/CLAUDE.md

@@ -0,0 +1,37 @@
+# CLAUDE.md
+
+## External-Interface Change Sign-Off
+
+This plugin's *external interface* is: cvalues external project configs can
+set/override, `<tool>` names, environment-script names, documented
+file-naming conventions, and public Groovy/Java API (classes/methods other
+plugins could extend or call).
+
+Before closing any task or change in this plugin, check whether it touches
+the external interface. If yes:
+
+1. Add/update a row in `docs/developers/ExternalInterfaceChangeLog.adoc`
+   describing the change and its risk if unconfirmed.
+2. Get explicit user sign-off before merging that change — do not silently
+   assume a breaking change is acceptable, even if it looks like dead or
+   already-broken code.
+
+Keep that table current for all changes, or whenever you notice it's
+drifted from the ground truth (the code) — not just when a task happens to
+touch it.
+
+This is a standing, cross-cutting process rule, not a one-shot task — apply
+it for the lifetime of this plugin's development, not just the current
+branch's task batch.
+
+### Version numbers in change documentation
+
+Never assert the version/tag a not-yet-released change will ship under
+(e.g. "new in 1.2.73-205") unless that number is already decided and fixed
+— branch-local "next version" labels are placeholders and the actual
+release tag (e.g. it could become 1.4.0 instead) is often undecided until
+release time. When documenting a still-unreleased addition, either omit the
+version or say it's "on this branch, not yet released under a tag". When
+documenting a removed/renamed/deprecated item, anchor on the last tag that
+is certain to have shipped it (e.g. "present up to and including
+1.2.73-204") rather than the uncertain next tag.

.claude/hooks/lintr-r-changes.sh

@@ -0,0 +1,16 @@
+#!/usr/bin/env bash
+set -ueo pipefail
+
+input="$(cat)"
+filePath="$(jq -r '.tool_input.file_path // .tool_response.filePath // empty' <<<"$input")"
+
+[[ "$filePath" =~ \.[Rr]$ ]] || exit 0
+[[ -f "$filePath" ]] || exit 0
+command -v Rscript >/dev/null 2>&1 || exit 0
+
+output="$(Rscript -e 'lints <- lintr::lint(commandArgs(trailingOnly = TRUE)[1]); if (length(lints) > 0) print(lints)' "$filePath" 2>&1)"
+
+[[ -z "$output" ]] && exit 0
+
+jq -n --arg ctx "lintr found issues in $filePath:
+$output" '{hookSpecificOutput: {hookEventName: "PostToolUse", additionalContext: $ctx}}'

.claude/hooks/shellcheck-bash-changes.sh

@@ -0,0 +1,15 @@
+#!/usr/bin/env bash
+set -ueo pipefail
+
+input="$(cat)"
+filePath="$(jq -r '.tool_input.file_path // .tool_response.filePath // empty' <<<"$input")"
+
+[[ "$filePath" == *.sh ]] || exit 0
+[[ -f "$filePath" ]] || exit 0
+
+if output="$(shellcheck "$filePath" 2>&1)"; then
+    exit 0
+fi
+
+jq -n --arg ctx "shellcheck found issues in $filePath:
+$output" '{hookSpecificOutput: {hookEventName: "PostToolUse", additionalContext: $ctx}}'

.claude/settings.json

@@ -0,0 +1,21 @@
+{
+  "hooks": {
+    "PostToolUse": [
+      {
+        "matcher": "Write|Edit",
+        "hooks": [
+          {
+            "type": "command",
+            "command": "\"$CLAUDE_PROJECT_DIR/.claude/hooks/shellcheck-bash-changes.sh\" 2>/dev/null || true",
+            "statusMessage": "Running shellcheck..."
+          },
+          {
+            "type": "command",
+            "command": "\"$CLAUDE_PROJECT_DIR/.claude/hooks/lintr-r-changes.sh\" 2>/dev/null || true",
+            "statusMessage": "Running lintr..."
+          }
+        ]
+      }
+    ]
+  }
+}

.gitignore

@@ -2,3 +2,6 @@ manifest.tmp
 build/
 out/
 shunit2/
+.claude/tasks/
+.claude/CLAUDE.local.md
+.claude/local/

AlignmentAndQCWorkflows_1.2.73-205.iml

@@ -0,0 +1,20 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<module type="JAVA_MODULE" version="4">
+  <component name="NewModuleRootManager" inherit-compiler-output="true">
+    <exclude-output />
+    <content url="file://$MODULE_DIR$">
+      <sourceFolder url="file://$MODULE_DIR$/docs" type="java-resource" />
+      <sourceFolder url="file://$MODULE_DIR$/resources/analysisTools" isTestSource="false" />
+      <sourceFolder url="file://$MODULE_DIR$/resources/configurationFiles" type="java-resource" />
+      <sourceFolder url="file://$MODULE_DIR$/resources/tests" isTestSource="true" />
+      <sourceFolder url="file://$MODULE_DIR$/src" isTestSource="false" />
+    </content>
+    <orderEntry type="inheritedJdk" />
+    <orderEntry type="sourceFolder" forTests="false" />
+    <orderEntry type="module" module-name="Roddy.main" />
+    <orderEntry type="library" name="Gradle: org.codehaus.groovy:groovy-all:2.4.21" level="project" />
+    <orderEntry type="module" module-name="BatchEuphoria.main" />
+    <orderEntry type="module" module-name="RoddyToolLib.main" />
+    <orderEntry type="module" module-name="COWorkflowsBasePlugin_1.4.2" />
+  </component>
+</module>

README.md

@@ -16,6 +16,18 @@ The original script with a documentation of the underlying ideas can be found [h
 
 ## Change Logs
 
+* 1.2.73-205 (branch-specific change)
+  - minor: Added `bwaPostAltJsK8Options` to allow setting opt K8 options for `bwa-postalt.js`
+  - minor: Upgrade from COWorkflows 1.2.76 to COWorkflowsBasePlugin 1.4.2.
+    - minor: Old `FLAG_USE_EXISTING_PAIRED_BAMS` was renamed to `FLAG_USE_ONLY_EXISTING_PAIRED_BAMS`
+    - minor: Removed `FLAG_RUN_SLIM_WORKFLOW`. Corresponding code is unused for years.
+  - patch: Added `SAM_SORT_MEMSIZE` to allow reducing memory for SAM sorting. Default: `500M` per thread (see issue #97: unbounded growth with ALT-contig/`bwa-postalt.js` processing was traced to `samtools sort`, not to `bwa-postalt.js` itself; bounding this cvalue fixes it for all alignment workflow runs, not only ALT-aware ones).
+      * `SAMPESORT_MEMSIZE` (the original name for this cvalue) is deprecated but still works: `SAM_SORT_MEMSIZE` defaults to `${SAMPESORT_MEMSIZE}`, so existing project configs that set the old name keep functioning unchanged.
+  - patch: Little refactorings and groovification of old Java code
+
+* 1.2.73-204 (branch-specific change)
+  - minor: Separate BWA from BWAKIT version. Default `BWAKIT_VERSION` to `BWA_VERSION`. Independently set `K8_VERSION` (default 0.2.5). Changed associated module-loading code in environment setup file `tbi-lsf-cluster.sh`.
+
 * 1.2.73-203 (branch-specific change)
   - minor: Optional ALT-chromosome processing via bwa.kit's `bwa-postaln.js`.
     * Set `runBwaPostAltJs=true` to activate the ALT chromosome processing. Default: `false`.

buildinfo.txt

@@ -1,4 +1,4 @@
-dependson=COWorkflows:1.2.76
+dependson=COWorkflowsBasePlugin:1.4.2
 JDKVersion=1.8
 GroovyVersion=2.4
-RoddyAPIVersion=3.0
+RoddyAPIVersion=3.7