Merge pull request #43 from maize-genetics/fix-nuqseqio-gz

Fix nuqseqio gz

Author: tcasstevens

.github/workflows/run-tests-on-pr.yml

@@ -17,6 +17,8 @@ jobs:
       checks: write # See: https://github.com/mikepenz/action-junit-report/issues/23#issuecomment-1412597753
     steps:
       - uses: actions/checkout@v3
+        with:
+          fetch-depth: 0
       - uses: actions/setup-java@v3
         with:
           distribution: temurin

src/main/kotlin/biokotlin/packages.md

@@ -132,7 +132,7 @@ of a transcript, you must know that it is a transcript.
 
 Parsing a GFF file to a tree requires only a single line:
 ```kotlin
-val genome = Genome.fromGFF("pathname.gff")
+val genome = Genome.fromFile("pathname.gff")
 ```
 
 GFFs that do not adhere to the structure will crash. Those that contain feature types that are not currently

src/main/kotlin/biokotlin/seqIO/SeqIO.kt

@@ -67,10 +67,8 @@ fun reader(filename: String, format: SeqFormat? = null, type: SeqType = SeqType.
         format
     } else {
 
-        val extension = File(filename).extension
-
         val guessFormat = SeqFormat.values().find {
-            it.suffixes.contains(extension)
+            it.suffixes.any { suffix -> filename.endsWith(suffix) }
         }
 
         guessFormat ?: throw IllegalArgumentException("Unknown file type: $filename")

src/test/kotlin/biokotlin/seqIO/SeqIOTest.kt

@@ -0,0 +1,20 @@
+package biokotlin.seqIO
+
+import io.kotest.core.spec.style.StringSpec
+import org.junit.jupiter.api.assertDoesNotThrow
+
+class SeqIOTest : StringSpec({
+
+    val fasta = "src/test/resources/biokotlin/seqIO/B73_Ref_Subset.fa"
+    val fastaZipped = "src/test/resources/biokotlin/seqIO/B73_Ref_Subset.fa.gz"
+    val fastq = "src/test/resources/biokotlin/seqIO/example.fq"
+    val fastqZipped = "src/test/resources/biokotlin/seqIO/example.fq.gz"
+
+    "Verify file type recognized" {
+        assertDoesNotThrow { NucSeqIO(fasta) }
+        assertDoesNotThrow { NucSeqIO(fastaZipped) }
+        assertDoesNotThrow { FastqIO(fastq) }
+        assertDoesNotThrow { FastqIO(fastqZipped) }
+    }
+
+})