Merge pull request #324 from wtsi-npg/devel

release 0.37.1 prep (merge devel to master)

Changes

@@ -1,6 +1,8 @@
 CHANGES LOG
 -----------
 
+ - updated to use samtools merge instead of bammerge for library merging  
+
 0.37.0
  - add i2b_nocall_qual_switch to stage1 analysis to enable "--nocall-quality=2" to be set for bambi i2b
 

data/vtlib/markdup_duplexseq.json

@@ -3,17 +3,36 @@
 "description":"steps in the alignment pipeline to post-process bam files produced by the AlignmentFilter",
 "subgraph_io":{
 	"ports":{
-		"inputs":{ "_stdin_":"bamsort_coord" },
+		"inputs":{ "_stdin_":"fixmate" },
 		"outputs":{ "_stdout_":"bammarkduplicates" }
 	}
 },
 "nodes":[
+	{
+		"id":"fixmate",
+		"type":"EXEC",
+		"use_STDIN": true,
+		"use_STDOUT": true,
+		"cmd": [
+			{"subst":"samtools_executable", "required":true, "ifnull":"samtools"}, "fixmate",
+			"--threads", {"subst":"fixmate_threads","required":true,"ifnull":4},
+			{"select":"fixmate_add_mate_score", "required":true, "select_range":[1], "default":"on", "cases":{"on":"-m","off":[]}},
+			{"subst":"fixmate_extra_flags", "required":false},
+			"-", "-"
+		]
+	},
 	{
 		"id":"bamsort_coord",
 		"type":"EXEC",
 		"use_STDIN": true,
 		"use_STDOUT": true,
-		"cmd": [ {"subst":"bsc_executable", "required":"yes", "ifnull":"bamsormadup"}, {"subst":"bsmd_threads"}, "SO=coordinate", "verbose=0", "fixmate=1", "rcsupport=1", {"subst":"bs_tmpfile_flag"} ]
+		"cmd": [
+			{"subst":"bsc_executable", "required":"yes", "ifnull":"bamsormadup"},
+			{"subst":"bsmd_threads"},
+			"SO=coordinate",
+			"verbose=0",
+			"rcsupport=1",
+			{"subst":"bs_tmpfile_flag"} ]
 	},
         {
                 "id":"calmd",
@@ -44,6 +63,7 @@
 	}
 ],
 "edges":[
+	{ "id":"fixmate_to_coordsort", "from":"fixmate", "to":"bamsort_coord" },
 	{ "id":"coordsort_to_calmd", "from":"bamsort_coord", "to":"calmd" },
 	{ "id":"calmd_to_markdup", "from":"calmd", "to":"bammarkduplicates" }
 ]

data/vtlib/merge_aligned.json

@@ -80,7 +80,7 @@
 		"use_STDIN": false,
 		"use_STDOUT": true,
 		"orig_cmd":{"subst":"crammerge"},
-		"cmd": [ "bammerge", "level=0", "SO=coordinate", "inputformat=cram", "outputformat=bam", {"subst":"incrams"} ],
+    "cmd": [ "samtools","merge","-O","BAM","-l","0","-",{"subst":"incrams"} ],
 		"description":"merge individual cram files from a sample into one cram file"
 	},
 	{