Don't import ref_cache/ external tool source code or mpileup2/*.[ch]

Omit the htslib/ref_cache/ source code, and hard-code a configure
--disable-ref-cache argument accordingly.

BCFtools's mpileup2/* is currently used only by plugins/vrfs.c which
we don't wrap, so we can (for now) omit this mpileup2/* code too.

Author: jmarshall

devtools/import.py

@@ -32,13 +32,14 @@
         "vcf-miniview.c",
     ),
     "bcftools": (
+        "mpileup2",
         "test", "plugins", "peakfit.c",
         "peakfit.h",
         "polysomy.c"),
     "htslib": (
         'annot-tsv.c', 'bgzip.c', 'htsfile.c', 'tabix.c',
         'hts_probe_cc.sh',
-        "samples", "test", "tests"),
+        "ref_cache", "samples", "test", "tests"),
 }
 
 

setup.py

@@ -61,8 +61,9 @@ def changedir(path):
 def run_configure(option):
     sys.stdout.flush()
     try:
+        # Always disable ref-cache as its code is omitted from pysam's htslib/
         retcode = subprocess.call(
-            " ".join(("./configure", option)),
+            " ".join(("./configure", "--disable-ref-cache", option)),
             shell=True)
         if retcode != 0:
             return False