Merge pull request #27 from hillerlab/rearrangement

Rearrangement
hillerlab · Sep 15, 2023 · 056546f · 056546f
2 parents 22a84f3 + 54782c0
commit 056546f
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diff --git a/.clocignore b/.clocignore
@@ -0,0 +1,11 @@
+# cloc --exclude-list-file=.clocignore .
+.vscode
+.DS_Store
+.idea
+venv
+test_out
+test_data
+old_backup
+HL_kent_binaries
+chainAxtIssue
+chain_clean_micro_env
diff --git a/.gitignore b/.gitignore
@@ -12,4 +12,25 @@ temp/*
 .DS_Store
 .idea/*
 venv/*
-.idea/*
+__pycache__/*
+modules/__pycache__/*
+*/__pycache__/
+
+# Kent binaries
+HL_kent_binaries/pslSortAcc
+HL_kent_binaries/chainAntiRepeat
+HL_kent_binaries/chainMergeSort
+HL_kent_binaries/chainCleaner
+HL_kent_binaries/chainSort
+HL_kent_binaries/chainScore
+chain_clean_micro_env/chainNet
+/HL_kent_binaries/chainFilter
+# to be continued
+
+# test data
+test_out/
+test_out_2/
+test_data/humanChrX.fa
+test_data/mm39ChrX.fa
+test_out_new/
+test_out_old/
diff --git a/.gitmodules b/.gitmodules
diff --git a/GenomeAlignmentTools b/GenomeAlignmentTools
diff --git a/HL_kent_binaries/chainExtractID.py b/HL_kent_binaries/chainExtractID.py
diff --git a/HL_kent_binaries/chainIndexID.py b/HL_kent_binaries/chainIndexID.py