From 215c699307a23fd7043116cfb13ccd0035fe812f Mon Sep 17 00:00:00 2001
From: Mike Renfro <mike+github@renf.ro>
Date: Mon, 9 Oct 2023 05:47:54 -0500
Subject: velvet: improved variants (#40225)

---
 var/spack/repos/builtin/packages/velvet/package.py | 49 +++++++++++++++++++++-
 1 file changed, 48 insertions(+), 1 deletion(-)

(limited to 'var')

diff --git a/var/spack/repos/builtin/packages/velvet/package.py b/var/spack/repos/builtin/packages/velvet/package.py
index 89b88feaff..55c76fee33 100644
--- a/var/spack/repos/builtin/packages/velvet/package.py
+++ b/var/spack/repos/builtin/packages/velvet/package.py
@@ -6,6 +6,13 @@
 from spack.package import *
 
 
+def is_positive_int(x):
+    if x.isdigit() and int(x) > 0:
+        return True
+    else:
+        return False
+
+
 class Velvet(MakefilePackage):
     """Velvet is a de novo genomic assembler specially designed for short read
     sequencing technologies."""
@@ -13,14 +20,54 @@ class Velvet(MakefilePackage):
     homepage = "https://www.ebi.ac.uk/~zerbino/velvet/"
     url = "https://www.ebi.ac.uk/~zerbino/velvet/velvet_1.2.10.tgz"
 
+    maintainers("snehring")
+
     version("1.2.10", sha256="884dd488c2d12f1f89cdc530a266af5d3106965f21ab9149e8cb5c633c977640")
 
+    variant(
+        "categories",
+        default="2",
+        description="Number of channels which can be handled independently",
+        values=is_positive_int,
+    )
+    variant(
+        "maxkmerlength",
+        default="31",
+        description="Longest kmer size you can use in an analysis",
+        values=is_positive_int,
+    )
+    variant("bigassembly", default=False, description="Allow assemblies with more than 2^31 reads")
+    variant(
+        "vbigassembly",
+        default=False,
+        description="Allow unsigned 64-bit array index values (also enables bigassembly)",
+    )
+    variant(
+        "longsequences", default=False, description="Allow assembling contigs longer than 32kb"
+    )
+    variant("openmp", default=False, description="Enable multithreading")
+    variant("single_cov_cat", default=False, description="Per-library coverage")
+
     depends_on("zlib-api")
 
     def edit(self, spec, prefix):
+        makefile = FileFilter("Makefile")
         if spec.target.family == "aarch64":
-            makefile = FileFilter("Makefile")
             makefile.filter("-m64", "")
+        maxkmerlength = self.spec.variants["maxkmerlength"].value
+        categories = self.spec.variants["categories"].value
+        makefile.filter(r"^MAXKMERLENGTH\s*=\s*.*", f"MAXKMERLENGTH = {maxkmerlength}")
+        makefile.filter(r"^CATEGORIES\s*=\s*.*", f"CATEGORIES = {categories}")
+        if "+bigassembly" in self.spec:
+            makefile.filter("^ifdef BIGASSEMBLY", "BIGASSEMBLY=1\nifdef BIGASSEMBLY")
+        if "+vbigassembly" in self.spec:
+            makefile.filter("^ifdef VBIGASSEMBLY", "VBIGASSEMBLY=1\nifdef VBIGASSEMBLY")
+        if "+longsequences" in self.spec:
+            makefile.filter("^ifdef LONGSEQUENCES", "LONGSEQUENCES=1\nifdef LONGSEQUENCES")
+        if "+openmp" in self.spec:
+            makefile.filter("^ifdef OPENMP", "OPENMP=1\nifdef OPENMP")
+        if "+single_cov_cat" in self.spec:
+            makefile.filter("^ifdef SINGLE_COV_CAT", "SINGLE_COV_CAT=1\nifdef SINGLE_COV_CAT")
 
     def install(self, spec, prefix):
         mkdirp(prefix.bin)
-- 
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