Merge pull request #48 from maize-genetics/merge-gvcfs-method-filenames

Added method mergeGVCFs that takes a list of input files. Existing me…

Author: tcasstevens

src/main/kotlin/biokotlin/util/MergeGVCFUtils.kt

@@ -25,11 +25,13 @@ private val myLogger = LogManager.getLogger("biokotlin.util.MergeGVCFUtils")
  */
 object MergeGVCFUtils {
 
-    fun mergeGVCFs(inputDir: String, outputFile: String, bedfile: String? = null) {
+    fun mergeGVCFs(inputDir: String, outputFile: String, bedFile: String? = null) {
+        mergeGVCFs(getGVCFFiles(inputDir), outputFile, bedFile)
+    }
 
-        runBlocking {
+    fun mergeGVCFs(inputFiles: List<String>, outputFile: String, bedFile: String? = null) {
 
-            val inputFiles = getGVCFFiles(inputDir)
+        runBlocking {
 
             require(validateVCFs(inputFiles).valid) { "Some GVCF files are invalid." }
 
@@ -70,12 +72,12 @@ object MergeGVCFUtils {
 
             }
 
-            val theBedfile = bedfile?.trim()
+            val theBedfile = bedFile?.trim()
             if (theBedfile.isNullOrEmpty()) {
                 myLogger.info("Writing output: $outputFile")
                 writeOutputVCF(outputFile, samples, variantContextChannel)
             } else {
-                myLogger.info("Writing output files with base name: $outputFile and bedfile: $bedfile")
+                myLogger.info("Writing output files with base name: $outputFile and bedfile: $bedFile")
                 writeOutputVCF(outputFile, theBedfile, samples, variantContextChannel)
             }