Run dos2unix on *.py and tidyup some files.

.gitignore

@@ -0,0 +1 @@
+*.pyc

ldsc_mod/ldscore/allele_info.py

@@ -1,63 +1,63 @@
-import itertools as it
-'''
-Contains useful objects related to allele relationships for ../munge_sumstats/py and sumstats.py
-
-'''
-
-_N_CHR = 22
-# complementary bases
-COMPLEMENT = {'A': 'T', 'T': 'A', 'C': 'G', 'G': 'C'}
-# bases
-BASES = COMPLEMENT.keys()
-# true iff strand ambiguous
-STRAND_AMBIGUOUS = {''.join(x): x[0] == COMPLEMENT[x[1]]
-                    for x in it.product(BASES, BASES)
-                    if x[0] != x[1]}
-# SNPS we want to keep (pairs of alleles)
-VALID_SNPS = {x for x in map(lambda y: ''.join(y), it.product(BASES, BASES))
-              if x[0] != x[1] and not STRAND_AMBIGUOUS[x]}
-
-VALID_andSA_SNPS = {x for x in map(lambda y: ''.join(y), it.product(BASES, BASES))
-              if x[0] != x[1]}
-
-# T iff SNP 1 has the same alleles as SNP 2 (allowing for strand or ref allele flip).
-MATCH_ALLELES = {x for x in map(lambda y: ''.join(y), it.product(VALID_SNPS, VALID_SNPS))
-                 # strand and ref match
-                 if ((x[0] == x[2]) and (x[1] == x[3])) or
-                 # ref match, strand flip
-                 ((x[0] == COMPLEMENT[x[2]]) and (x[1] == COMPLEMENT[x[3]])) or
-                 # ref flip, strand match
-                 ((x[0] == x[3]) and (x[1] == x[2])) or
-                 ((x[0] == COMPLEMENT[x[3]]) and (x[1] == COMPLEMENT[x[2]]))}  # strand and ref flip
-# T iff SNP 1 has the same alleles as SNP 2 w/ ref allele flip.
-FLIP_ALLELES = {''.join(x):
-                ((x[0] == x[3]) and (x[1] == x[2])) or  # strand match
-                # strand flip
-                ((x[0] == COMPLEMENT[x[3]]) and (x[1] == COMPLEMENT[x[2]]))
-                for x in MATCH_ALLELES}
-
-
-__version__ = '1.0.0'
-MASTHEAD = "*********************************************************************\n"
-MASTHEAD += "* LD Score Regression (LDSC)\n"
-MASTHEAD += "* Version {V}\n".format(V=__version__)
-MASTHEAD += "* (C) 2014-2015 Brendan Bulik-Sullivan and Hilary Finucane\n"
-MASTHEAD += "* Broad Institute of MIT and Harvard / MIT Department of Mathematics\n"
-MASTHEAD += "* GNU General Public License v3\n"
-MASTHEAD += "*********************************************************************\n"
-
-
-def sec_to_str(t):
-    '''Convert seconds to days:hours:minutes:seconds'''
-    [d, h, m, s, n] = reduce(lambda ll, b : divmod(ll[0], b) + ll[1:], [(t, 1), 60, 60, 24])
-    f = ''
-    if d > 0:
-        f += '{D}d:'.format(D=d)
-    if h > 0:
-        f += '{H}h:'.format(H=h)
-    if m > 0:
-        f += '{M}m:'.format(M=m)
-
-    f += '{S}s'.format(S=s)
-    return f
-
+import itertools as it
+'''
+Contains useful objects related to allele relationships for ../munge_sumstats/py and sumstats.py
+
+'''
+
+_N_CHR = 22
+# complementary bases
+COMPLEMENT = {'A': 'T', 'T': 'A', 'C': 'G', 'G': 'C'}
+# bases
+BASES = COMPLEMENT.keys()
+# true iff strand ambiguous
+STRAND_AMBIGUOUS = {''.join(x): x[0] == COMPLEMENT[x[1]]
+                    for x in it.product(BASES, BASES)
+                    if x[0] != x[1]}
+# SNPS we want to keep (pairs of alleles)
+VALID_SNPS = {x for x in map(lambda y: ''.join(y), it.product(BASES, BASES))
+              if x[0] != x[1] and not STRAND_AMBIGUOUS[x]}
+
+VALID_andSA_SNPS = {x for x in map(lambda y: ''.join(y), it.product(BASES, BASES))
+              if x[0] != x[1]}
+
+# T iff SNP 1 has the same alleles as SNP 2 (allowing for strand or ref allele flip).
+MATCH_ALLELES = {x for x in map(lambda y: ''.join(y), it.product(VALID_SNPS, VALID_SNPS))
+                 # strand and ref match
+                 if ((x[0] == x[2]) and (x[1] == x[3])) or
+                 # ref match, strand flip
+                 ((x[0] == COMPLEMENT[x[2]]) and (x[1] == COMPLEMENT[x[3]])) or
+                 # ref flip, strand match
+                 ((x[0] == x[3]) and (x[1] == x[2])) or
+                 ((x[0] == COMPLEMENT[x[3]]) and (x[1] == COMPLEMENT[x[2]]))}  # strand and ref flip
+# T iff SNP 1 has the same alleles as SNP 2 w/ ref allele flip.
+FLIP_ALLELES = {''.join(x):
+                ((x[0] == x[3]) and (x[1] == x[2])) or  # strand match
+                # strand flip
+                ((x[0] == COMPLEMENT[x[3]]) and (x[1] == COMPLEMENT[x[2]]))
+                for x in MATCH_ALLELES}
+
+
+__version__ = '1.0.0'
+MASTHEAD = "*********************************************************************\n"
+MASTHEAD += "* LD Score Regression (LDSC)\n"
+MASTHEAD += "* Version {V}\n".format(V=__version__)
+MASTHEAD += "* (C) 2014-2015 Brendan Bulik-Sullivan and Hilary Finucane\n"
+MASTHEAD += "* Broad Institute of MIT and Harvard / MIT Department of Mathematics\n"
+MASTHEAD += "* GNU General Public License v3\n"
+MASTHEAD += "*********************************************************************\n"
+
+
+def sec_to_str(t):
+    '''Convert seconds to days:hours:minutes:seconds'''
+    [d, h, m, s, n] = reduce(lambda ll, b : divmod(ll[0], b) + ll[1:], [(t, 1), 60, 60, 24])
+    f = ''
+    if d > 0:
+        f += '{D}d:'.format(D=d)
+    if h > 0:
+        f += '{H}h:'.format(H=h)
+    if m > 0:
+        f += '{M}m:'.format(M=m)
+
+    f += '{S}s'.format(S=s)
+    return f
+