Merge pull request #47 from 4dn-dcic/0.3.0

0.3.0

README.md

@@ -609,14 +609,18 @@ ulimit -n 2000
 
 ## Version history
 
+### 0.3.0
+* The problem with `fragment_4dnpairs.pl` of adding an extra column is now fixed.
+* Fixed bug with 1D querying on 2D data.
+
 ### 0.2.9
 * `pairix` can now take 1D query for 2D data. e.g.) `pairix file.gz 'chr22:50000-60000'` is equivalent to `pairix file.gz 'chr22:50000-60000|chr22:50000-60000'` if file.gz is 2D indexed.
 
 ### 0.2.8
 * `pairix` now has option `-a` (autoflip) that flips the query in case the matching chromosome pair doesn't exist in the file.
 * `pairix` now has option `-W` that prints out region split character use for indexing a specific file.
 * `merge-pairs.sh` is now included in `util`.
-* ~`pairix` can now take 1D query for 2D data. e.g.) `pairix file.gz 'chr22:50000-60000'` is equivalent to `pairix file.gz 'chr22:50000-60000|chr22:50000-60000'` if file.gz is 2D indexed.~  This one currently does not work. 
+* ~`pairix` can now take 1D query for 2D data. e.g.) `pairix file.gz 'chr22:50000-60000'` is equivalent to `pairix file.gz 'chr22:50000-60000|chr22:50000-60000'` if file.gz is 2D indexed.~  This one currently does not work.
 
 ### 0.2.6
 * Two utils are added: `duplicate_header_remover.pl` and `column_remover.pl` for pairs file format correction.

VERSION.txt

@@ -1 +1 @@
-0.2.9
+0.3.0

src/pairix.h

@@ -28,7 +28,7 @@
 #ifndef __TABIDX_H
 #define __TABIDX_H
 
-#define PACKAGE_VERSION "0.2.9"
+#define PACKAGE_VERSION "0.3.0"
 
 #include <stdint.h>
 #include "kstring.h"

test/test.py

@@ -18,7 +18,7 @@
 4DN: chr1[1] pos1[2] chr2[3] pos2[4]
 """
 
-
+from __future__ import unicode_literals
 import unittest
 import gzip
 import sys
@@ -150,17 +150,17 @@ def get_result(regions, chrom, start, end):
 
 def get_result_2D(regions, chrom, start, end, chrom2, start2, end2):
     retval = []
-    for r in regions:
-        if r[0] == chrom and overlap1(r[1], r[2], start, end) and r[3] == chrom2 and overlap1(r[4], r[5], start2, end2):
-            retval.append(r)
+    for reg in regions:
+        if reg[0] == chrom and overlap1(reg[1], reg[2], start, end) and reg[3] == chrom2 and overlap1(reg[4], reg[5], start2, end2):
+            retval.append(reg)
     return retval
 
 
-def get_result_2D_4DN(regions, chrom, start, end, chrom2, start2, end2):
+def get_result_1D_on_2D(regions, chrom, start, end, chrom2, start2, end2):
     retval = []
-    for r in regions:
-        if r[1] == chrom and overlap1(r[2], r[2], start, end) and r[3] == chrom2 and overlap1(r[4], r[4], start2, end2):
-            retval.append(r)
+    for reg in regions:
+        if reg[0] == chrom and overlap1(reg[2], reg[2], start, end) and reg[3] == chrom2 and overlap1(reg[4], reg[4], start2, end2):
+            retval.append(reg)
     return retval
 
 
@@ -409,7 +409,7 @@ class PairixTest_1_on_2(unittest.TestCase):
     chrom2 = chrom
     start2 = start
     end2 = end
-    result = get_result_2D_4DN(regions, chrom, start, end, chrom2, 0, sys.maxsize)
+    result = get_result_1D_on_2D(regions, chrom, start, end, chrom2, start2, end2)
     pr = pypairix.open(TEST_FILE_2D_4DN_2)
 
     def test_querys(self):

util/fragment_4dnpairs.pl

@@ -91,11 +91,11 @@
               elsif($headers[$i] eq 'frag2') { $frag2_colindex=$i-1; }
           }
           print STDERR "$frag1_colindex, $frag2_colindex\n";  # Soo
-          if($frag1_colindex == -1) { $frag1_colindex=$#headers+1; print OUTFILE "$_ frag1\n"; next; }
-          elsif($frag2_colindex == -1) { $frag2_colindex=$#headers+1; print OUTFILE "$_ frag2\n"; next; }
+          if($frag1_colindex == -1) { $frag1_colindex=$#headers; print OUTFILE "$_ frag1\n"; next; }
+          elsif($frag2_colindex == -1) { $frag2_colindex=$#headers; print OUTFILE "$_ frag2\n"; next; }
           else { print OUTFILE "$_\n"; next; }
       }
-      else { $frag1_colindex=$#headers+1; $frag2_colindex=$#headers+2; print OUTFILE "$_ frag1 frag2\n"; next; }
+      else { $frag1_colindex=$#headers; $frag2_colindex=$#headers+1; print OUTFILE "$_ frag1 frag2\n"; next; }
   }
   elsif(/^#/) { print OUTFILE "$_\n"; next; }
   my @original_record = split;