pbwt: new package (#49055)

* pbwt: add v2.1, v2.0

Signed-off-by: Teague Sterling <teaguesterling@gmail.com>

* [@spackbot] updating style on behalf of teaguesterling

* Update package.py

---------

Signed-off-by: Teague Sterling <teaguesterling@gmail.com>

var/spack/repos/builtin/packages/pbwt/package.py

@@ -0,0 +1,41 @@
+# Copyright Spack Project Developers. See COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack.package import *
+
+
+class Pbwt(MakefilePackage):
+    """Implementation of Positional Burrows-Wheeler Transform for genetic data."""
+
+    homepage = "https://github.com/richarddurbin/pbwt"
+    url = "https://github.com/richarddurbin/pbwt/archive/refs/tags/v2.1.tar.gz"
+
+    maintainers("teaguesterling")
+
+    license("APACHE-2.0", checked_by="teaguesterling")  # License in pbwtCore.c
+
+    version("2.1", sha256="d48ff12a0a84b1eb8ba5081fd900b5d003cfacc44b5a3d35a1423c69cc3f3e90")
+    version("2.0", sha256="3750e355989fdc4e646d68dfe2dd7262ac3da46a2bff66c8563443fb44ecaf96")
+
+    depends_on("c", type="build")
+    depends_on("htslib")
+    depends_on("zlib-api")
+    depends_on("bzip2")
+    depends_on("lzma")
+    depends_on("curl")
+
+    def patch(self):
+        htslib = self.spec["htslib"]
+        filter_file("^HTSDIR=../htslib$", f"HTSDIR={htslib.prefix}", "Makefile")
+        filter_file(r"^CPPFLAGS=-I\$\(HTSDIR\)$", r"CPPFLAGS=-I$(HTSDIR)/include", "Makefile")
+        filter_file(r"^HTSLIB=\$\(HTSDIR\)/libhts.a$", "HTSLIB=$(HTSDIR)/lib/libhts.a", "Makefile")
+        filter_file(
+            r"^LDLIBS=-lpthread \$\(HTSLIB\) -lz -lm -lbz2 -llzma -lcurl$",
+            "LDLIBS=-lpthread $(HTSLIB) -lz -lm -lbz2 -llzma -lcurl -lcrypto -ldeflate",
+            "Makefile",
+        )
+
+    @property
+    def install_targets(self):
+        return ["install", f"PREFIX={self.prefix.bin}"]