Updating docs to match the code.

mkdocs.yml

@@ -84,7 +84,7 @@ nav:
       - Building and loading: build_and_load.md
       - Imputation:
           - k-mer Imputation (Original): imputation.md
-          - RopeBWT3 Imputation (BETA): ropebwt3_imputation.md
+          - RopeBWT3 Imputation (BETA): imputation_ropebwt.md
       - Resequencing: resequencing.md
       - Exporting data: export_data.md
   - Reference:

src/main/kotlin/net/maizegenetics/phgv2/cli/Phg.kt

@@ -7,7 +7,7 @@ import com.github.ajalt.clikt.output.MordantHelpFormatter
 import com.github.ajalt.clikt.parameters.options.versionOption
 import net.maizegenetics.phgv2.pathing.*
 import net.maizegenetics.phgv2.pathing.ropebwt.MapReads
-import net.maizegenetics.phgv2.pathing.ropebwt.RopebwtIndex
+import net.maizegenetics.phgv2.pathing.ropebwt.RopeBwtIndex
 import net.maizegenetics.phgv2.utils.phgVersion
 import net.maizegenetics.phgv2.utils.setupDebugLogging
 
@@ -33,7 +33,7 @@ fun main(args: Array<String>) = Phg()
         SetupEnvironment(), Initdb(), CreateRanges(), PrepareAssemblies(), AgcCompress(), AlignAssemblies(), PrepareSlurmAlignFile(),
         CreateAnchorwaveDotplot(), CreateRefVcf(), CreateMafVcf(), Gvcf2Hvcf(), Hvcf2Gvcf(), LoadVcf(), ExportVcf(),
         BuildKmerIndex(), MapKmers(), FindPaths(), HapidSampleTable(), SampleHapidByRange(),
-        RopebwtIndex(), MapReads(), // Imputation
+        RopeBwtIndex(), MapReads(), // Imputation
         CreateFastaFromHvcf(), ListSamples(), MergeHvcfs(), MergeGVCFs(), CalcVcfMetrics(), StartServer, ExtractEdgeReads(), //Utilities
         QcReadMapping(), PathsToGff(), // Utilities continued
         CompositeToHaplotypeCoords(), // resequencing pipeline

src/main/kotlin/net/maizegenetics/phgv2/pathing/ropebwt/MapReads.kt

@@ -169,7 +169,9 @@ class MapReads : CliktCommand(help="BETA: Map reads to a pangenome using ropeBWT
             currentLine = bedFileReader.readLine()
         }
 
-        processMemsForRead(tempMems, readMapping, maxNumHits, hapIdToRefRangeMap)
+        if(tempMems.isNotEmpty()) {
+            processMemsForRead(tempMems, readMapping, maxNumHits, hapIdToRefRangeMap)
+        }
         return readMapping
     }
 

src/main/kotlin/net/maizegenetics/phgv2/pathing/ropebwt/RopebwtIndex.kt → src/main/kotlin/net/maizegenetics/phgv2/pathing/ropebwt/RopeBwtIndex.kt

@@ -33,9 +33,9 @@ sealed class RopeBWTIndexInput {
  *
  * With the output files we can then run ropebwt3 mem and get read mappings.
  */
-class RopebwtIndex : CliktCommand(help="BETA: Create a ropeBWT3 index") {
+class RopeBwtIndex : CliktCommand(help="BETA: Create a ropeBWT3 index") {
 
-    private val myLogger = LogManager.getLogger(RopebwtIndex::class.java)
+    private val myLogger = LogManager.getLogger(RopeBwtIndex::class.java)
 
     // Pre-compile the Regex pattern - used when creating the output fasta file names
     val HVCF_PATTERN = Regex("""(\.hvcf|\.h\.vcf|\.hvcf\.gz|\.h\.vcf\.gz)$""")
@@ -61,7 +61,7 @@ class RopebwtIndex : CliktCommand(help="BETA: Create a ropeBWT3 index") {
     val indexFilePrefix by option(help = "Prefix of the ropebwt3 index file.  This will be added to the output directory and ropeBWT3 will make a number of output files.")
         .required()
 
-    val numThreads by option(help = "Number of threads to use for the index creation.")
+    val threads by option(help = "Number of threads to use for the index creation.")
         .int()
         .default(3)
 
@@ -86,7 +86,7 @@ class RopebwtIndex : CliktCommand(help="BETA: Create a ropeBWT3 index") {
 
         myLogger.info("Creating ropeBWT3 index for $pangenomeFastaFile")
 
-        createInitialIndex(pangenomeFastaFile, "${outputDir}/${indexFilePrefix}", numThreads, deleteFmrIndex, condaEnvPrefix)
+        createInitialIndex(pangenomeFastaFile, "${outputDir}/${indexFilePrefix}", threads, deleteFmrIndex, condaEnvPrefix)
 
     }
 

src/test/kotlin/net/maizegenetics/phgv2/pathing/ropebwt/RopebwtIndexTest.kt → src/test/kotlin/net/maizegenetics/phgv2/pathing/ropebwt/RopeBwtIndexTest.kt

@@ -3,21 +3,15 @@
 import biokotlin.seqIO.NucSeqIO
 import biokotlin.util.bufferedReader
 import com.github.ajalt.clikt.testing.test
-import net.maizegenetics.phgv2.cli.AgcCompress
-import net.maizegenetics.phgv2.cli.CreateFastaFromHvcf
 import net.maizegenetics.phgv2.cli.TestExtension
 import net.maizegenetics.phgv2.utils.setupDebugLogging
 import org.junit.jupiter.api.AfterAll
 import org.junit.jupiter.api.BeforeAll
 import org.junit.jupiter.api.Test
-import java.io.BufferedWriter
 import java.io.File
-import java.io.FileWriter
-import kotlin.test.Ignore
 import kotlin.test.assertEquals
-import kotlin.test.fail
 
-class RopebwtIndexTest {
+class RopeBwtIndexTest {
 
 
     companion object {
@@ -64,7 +58,7 @@
 
     @Test
     fun testCliktParams() {
-        val ropebwtIndex = RopebwtIndex()
+        val ropebwtIndex = RopeBwtIndex()
 
 
         //pangenome-file
@@ -72,7 +66,7 @@
         //Leave off the input files
         val noInputs = ropebwtIndex.test("--db-path ${TestExtension.tempDir} --output-dir ${TestExtension.tempDir}ropebwtTest/ --index-file-prefix testIndex --num-threads 3 --delete-fmr-index")
         assertEquals(1, noInputs.statusCode)
         assertEquals("Usage: ropebwt-index [<options>]\n\n" +
                 "Error: must provide one of --pangenome-file, --hvcf-dir\n", noInputs.stderr)
 
         val tooManyInputs = ropebwtIndex.test("--pangenome-file data/test/smallseq/pangenome.fa --hvcf-dir data/test/smallseq/hvcf/ --db-path ${TestExtension.tempDir} --output-dir ${TestExtension.tempDir}ropebwtTest/ --index-file-prefix testIndex --num-threads 3 --delete-fmr-index")
@@ -97,7 +91,7 @@
     //runBuildStep(inputFasta:String, indexFilePrefix:String, numThreads: Int, condaEnvPrefix:String)
     @Test
     fun testRunBuildStep() {
-        val ropebwtIndex = RopebwtIndex()
+        val ropebwtIndex = RopeBwtIndex()
         val numThreads = 3
         ropebwtIndex.runBuildStep(inputFasta, indexFilePrefix, numThreads, "")
 
@@ -109,7 +103,7 @@
     //deleteFMRIndex(indexFilePrefix: String)
     @Test
     fun testConvertAndDeleteBWTIndex() {
-        val ropebwtIndex = RopebwtIndex()
+        val ropebwtIndex = RopeBwtIndex()
         val numThreads = 3
 
         ropebwtIndex.runBuildStep(inputFasta, indexFilePrefix, numThreads, "")
@@ -126,7 +120,7 @@
     //buildSuffixArray(indexFilePrefix: String, numThreads: Int, condaEnvPrefix: String)
     @Test
     fun testBuildSuffixArray() {
-        val ropebwtIndex = RopebwtIndex()
+        val ropebwtIndex = RopeBwtIndex()
         val numThreads = 3
 
         ropebwtIndex.runBuildStep(inputFasta, indexFilePrefix, numThreads, "")
@@ -139,7 +133,7 @@
     //buildChrLengthFile(inputFasta: String, indexFilePrefix: String)
     @Test
     fun testBuildChrLengthFile() {
-        val ropebwtIndex = RopebwtIndex()
+        val ropebwtIndex = RopeBwtIndex()
         ropebwtIndex.buildChrLengthFile(inputFasta, indexFilePrefix)
 
         //verify that the output file exists
@@ -167,7 +161,7 @@
     @Test
     fun createInitialIndex() {
         resetDirs()
-        val ropebwtIndex = RopebwtIndex()
+        val ropebwtIndex = RopeBwtIndex()
         val numThreads = 3
         ropebwtIndex.createInitialIndex(inputFasta, indexFilePrefix, numThreads, true,"")