Merge branch 'pantools_v3.1' into pantools_v3

e5f30dea · Workum, Dirk-Jan van · c9376adb · 4b27c1db · e5f30dea · c9376adb
Commit e5f30dea authored Nov 28, 2022 by Workum, Dirk-Jan van
--- a/.gitignore
+++ b/.gitignore
+*.class
+*.jar
+
--- a/Log
+++ b/Log
--- a/build/built-jar.properties
+++ b/build/built-jar.properties
-#Tue, 23 Mar 2021 14:19:20 +0100
+#Tue, 16 Nov 2021 10:49:29 +0100


-/mnt/LTR_userdata/jonkh004/pantools_v3_compile/pantools=
+/local/jonkh004/merge/pantools=
--- a/build/classes/alignment/BoundedLocalSequenceAlignment.class
+++ b/build/classes/alignment/BoundedLocalSequenceAlignment.class
--- a/build/classes/alignment/LocalSequenceAlignment.class
+++ b/build/classes/alignment/LocalSequenceAlignment.class
--- a/build/classes/index/IndexDatabase.class
+++ b/build/classes/index/IndexDatabase.class
--- a/build/classes/index/IndexPointer.class
+++ b/build/classes/index/IndexPointer.class
--- a/build/classes/index/IndexScanner.class
+++ b/build/classes/index/IndexScanner.class
--- a/build/classes/index/kmer.class
+++ b/build/classes/index/kmer.class
--- a/build/classes/pangenome/AnnotationLayer$IntPairComparator.class
+++ b/build/classes/pangenome/AnnotationLayer$IntPairComparator.class
--- a/build/classes/pangenome/AnnotationLayer$feature.class
+++ b/build/classes/pangenome/AnnotationLayer$feature.class
--- a/build/classes/pangenome/AnnotationLayer.class
+++ b/build/classes/pangenome/AnnotationLayer.class
--- a/build/classes/pangenome/Classification$multi_thread_find_shared_kmers.class
+++ b/build/classes/pangenome/Classification$multi_thread_find_shared_kmers.class
--- a/build/classes/pangenome/Classification$multi_thread_pangenome_size_gene.class
+++ b/build/classes/pangenome/Classification$multi_thread_pangenome_size_gene.class
--- a/build/classes/pangenome/Classification$multi_thread_pangenome_size_kmer.class
+++ b/build/classes/pangenome/Classification$multi_thread_pangenome_size_kmer.class
--- a/build/classes/pangenome/Classification.class
+++ b/build/classes/pangenome/Classification.class
--- a/build/classes/pangenome/ExecCommand$ErrorReader.class
+++ b/build/classes/pangenome/ExecCommand$ErrorReader.class
--- a/build/classes/pangenome/ExecCommand$InputWriter.class
+++ b/build/classes/pangenome/ExecCommand$InputWriter.class
--- a/build/classes/pangenome/ExecCommand$OutputReader.class
+++ b/build/classes/pangenome/ExecCommand$OutputReader.class
--- a/build/classes/pangenome/ExecCommand.class
+++ b/build/classes/pangenome/ExecCommand.class