Correct option docs from MANTA-1487

CHANGELOG.md

@@ -1,5 +1,5 @@
 ## v1.6.0 - 2019-06-25
-This is a significant engineering update from the v1.5.x release, in which the SV candidate generation step has been changed to a single multi-threaded process to improve task scheduling. This slightly improves average runtime and reduces runtime variability. With this update, support for job distribution over SGE is dropped.
+This is a significant engineering update from the v1.5.1 release, in which the SV candidate generation step has been changed to a single multi-threaded process to improve task scheduling. This slightly improves average runtime and reduces runtime variability. With this update, support for job distribution over SGE is dropped.
 
 ### Added
 - Add configuration option to turn off the evidence signal filter during candidate generation (DRAGEN-1873)
@@ -16,13 +16,13 @@ This is a significant engineering update from the v1.5.x release, in which the S
 This is a minor update from v1.5.0.
 
 ### Changed
-- Make existingAlignmentStats as a fallback option (MANTA-1487)
-  - It prioritizes stats estimated from the alignment file and allows static stats file when stats estimation fails due to insufficient high-confidence read pairs.
+- Change behavior of existingAlignmentStats option (MANTA-1487)
+  - Alignment statistics provided by this option will only be used as a default when direct estimation from the sample fails.
 - Minor updates on Methods writeup (MANTA-1522)
 
 ### Fixed
 - Fix a bug in selecting large insertion candidates (MANTA-1496)
-- Fix a minor bug in QC small SV alignment (MANTA-1498)
+- Fix a minor bug in QC small alignment SV (MANTA-1498)
 
 ## v1.5.0 - 2018-11-12
 This is a major update from v1.4.0, featuring improved precision and stability, a new configurable option of overlapping pair reads, and a few bug fixes. VCF representation is improved by introducing a couple of new filters and representing inversions as two breakend records.

docs/userGuide/README.md

@@ -662,9 +662,6 @@ These options are useful for Manta development and debugging:
 * The `--generateEvidenceBam` option can be used to generate bam files
   of evidence reads for SVs listed in the candidate vcf file.
   (More details in the section "Generating evidence bams" below)
-* The `--default-stats-file` option can be used to provide a file
-  containing read group statistics for Manta to fall back on when stats
-  estimation fails due to insufficient high-confidence read pairs.
 
 
 ### Extended use cases

src/python/bin/configManta.py

@@ -74,9 +74,9 @@ def addWorkflowGroupOptions(self,group) :
 
 
     def addExtendedGroupOptions(self,group) :
-        group.add_option("--existingAlignStatsFile",
-                         dest="existingAlignStatsFile", metavar="FILE",
-                         help="Pre-calculated alignment statistics file. Skips alignment stats calculation.")
+        group.add_option("--defaultAlignStatsFile", "--existingAlignStatsFile",
+                         dest="defaultAlignStatsFile", metavar="FILE",
+                         help="Default alignment statistics to use when direct estimation from the sample fails")
         group.add_option("--useExistingChromDepths",
                          dest="useExistingChromDepths", action="store_true",
                          help="Use pre-calculated chromosome depths.")
@@ -102,7 +102,7 @@ def getOptionDefaults(self) :
             'isRNA' : False,
             'isOutputContig' : False,
             'isUnstrandedRNA' : False,
-            'existingAlignStatsFile' : None,
+            'defaultAlignStatsFile' : None,
             'useExistingChromDepths' : False,
             'isRetainTempFiles' : False,
             'isGenerateSupportBam' : False
@@ -136,8 +136,8 @@ def safeLen(x) :
             if options.isUnstrandedRNA :
                 raise OptParseException("Unstranded only applied for RNA inputs")
 
-        if options.existingAlignStatsFile is not None :
-            options.existingAlignStatsFile=validateFixExistingFileArg(options.existingAlignStatsFile,"existing align stats")
+        if options.defaultAlignStatsFile is not None :
+            options.defaultAlignStatsFile=validateFixExistingFileArg(options.defaultAlignStatsFile,"default align stats")
 
         groomBamList(options.normalBamList,"normal sample")
         groomBamList(options.tumorBamList, "tumor sample")

src/python/lib/mantaWorkflow.py

@@ -174,12 +174,6 @@ def summarizeStats(self, taskPrefix="", dependencies=None) :
 
     return summaryTasks
 
-def copyStats(self) :
-    statsPath=self.paths.getStatsPath()
-    existingStatsPath=self.params.existingAlignStatsFile
-
-    shutil.copy(existingStatsPath, statsPath)
-
 def runStats(self,taskPrefix="",dependencies=None) :
 
     statsPath=self.paths.getStatsPath()
@@ -201,8 +195,8 @@ def runStats(self,taskPrefix="",dependencies=None) :
         cmd.extend(["--ref", self.params.referenceFasta])
         cmd.extend(["--output-file",tmpStatsFiles[-1]])
         cmd.extend(["--align-file",bamPath])
-        if self.params.existingAlignStatsFile:
-            cmd.extend(["--default-stats-file",self.params.existingAlignStatsFile])
+        if self.params.defaultAlignStatsFile:
+            cmd.extend(["--default-stats-file",self.params.defaultAlignStatsFile])
 
         statsTasks.add(self.addTask(preJoin(taskPrefix,"generateStats_"+indexStr),cmd,dependencies=dirTask))