From fc57448cee74e220eab93afa256d369dd541ba92 Mon Sep 17 00:00:00 2001
From: Carl Vitzthum <carl.vitzthum@gmail.com>
Date: Thu, 30 May 2019 15:57:29 -0400
Subject: [PATCH 1/2] 0.7.2 -- pass used_chrs to parse_hic for correct
 chromsome naming in warning

---
 README.md                  |  2 ++
 hic2cool/_version.py       |  2 +-
 hic2cool/hic2cool_utils.py | 16 +++++++++-------
 3 files changed, 12 insertions(+), 8 deletions(-)

diff --git a/README.md b/README.md
index 4017f88..cfb77df 100644
--- a/README.md
+++ b/README.md
@@ -124,6 +124,8 @@ You may also provide the optional `-e` flag, which will cause the mitchondrial c
 
 
 ## Changelog
+### 0.7.2
+* Warning from `parse_hic` will now output chromsome names, not indexes
 ### 0.7.1
 * Add `format` and `format-version` to `/` collection for multi-resolution coolers written by hic2cool
 * Run `hic2cool_update` to add these attributes to mcool files generated with previous hic2cool versions
diff --git a/hic2cool/_version.py b/hic2cool/_version.py
index a5f830a..bc8c296 100644
--- a/hic2cool/_version.py
+++ b/hic2cool/_version.py
@@ -1 +1 @@
-__version__ = "0.7.1"
+__version__ = "0.7.2"
diff --git a/hic2cool/hic2cool_utils.py b/hic2cool/hic2cool_utils.py
index b49ef14..3c0ec00 100755
--- a/hic2cool/hic2cool_utils.py
+++ b/hic2cool/hic2cool_utils.py
@@ -308,8 +308,8 @@ def read_normalization_vector(f, buf, entry):
     return np.frombuffer(buf, dtype=np.dtype('<d'), count=nValues, offset=filepos+4)
 
 
-def parse_hic(req, buf, outfile, chr_key, unit, binsize,
-              pair_footer_info, chr_offset_map, chr_bins, show_warnings):
+def parse_hic(req, buf, outfile, chr_key, unit, binsize, pair_footer_info,
+              chr_offset_map, chr_bins, used_chrs, show_warnings):
     """
     Adapted from the straw() function in the original straw package.
     Mainly, since all chroms are iterated over, the read_header and read_footer
@@ -332,8 +332,10 @@ def parse_hic(req, buf, outfile, chr_key, unit, binsize,
     except KeyError:
         WARN = True
         if show_warnings:
-            print_stderr('... The intersection between chr %s and chr %s cannot be found in the hic file.'
-                  % (c1, c2))
+            c1_name = used_chrs[c1][1]
+            c2_name = used_chrs[c2][1]
+            print_stderr('... The intersection between %s and %s cannot be found in the hic file.'
+                         % (c1_name, c2_name))
         return join_chunk
     region_indices = [0, chr_bins[c1], 0, chr_bins[c2]]
     myFilePos = pair_footer_info[chr_key]
@@ -900,9 +902,9 @@ def hic2cool_convert(infile, outfile, resolution=0, show_warnings=False, silent=
                 # and c2-c1 reciprocally
                 if chr_key in covered_chr_pairs:
                     continue
-                tmp_chunk = parse_hic(req, buf, outfile, chr_key,
-                          unit, binsize, pair_footer_info,
-                          chr_offset_map, chr_bins, show_warnings)
+                tmp_chunk = parse_hic(req, buf, outfile, chr_key, unit, binsize,
+                                      pair_footer_info, chr_offset_map, chr_bins,
+                                      used_chrs, show_warnings)
                 total_chunk = np.concatenate((total_chunk, tmp_chunk), axis=0)
                 del tmp_chunk
                 covered_chr_pairs.append(chr_key)

From 962bca392cc7770c8e6fc0189281a51f008d2d92 Mon Sep 17 00:00:00 2001
From: Carl Vitzthum <carl.vitzthum@gmail.com>
Date: Thu, 30 May 2019 21:08:32 -0400
Subject: [PATCH 2/2] Update README.md

---
 README.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/README.md b/README.md
index cfb77df..a02e828 100644
--- a/README.md
+++ b/README.md
@@ -125,7 +125,7 @@ You may also provide the optional `-e` flag, which will cause the mitchondrial c
 
 ## Changelog
 ### 0.7.2
-* Warning from `parse_hic` will now output chromsome names, not indexes
+* Warning from `hic2cool_utils.parse_hic` will now output chromsome names, not indices
 ### 0.7.1
 * Add `format` and `format-version` to `/` collection for multi-resolution coolers written by hic2cool
 * Run `hic2cool_update` to add these attributes to mcool files generated with previous hic2cool versions