Merge branch 'release/v.0.2.9'

.gitignore

@@ -1,4 +1,6 @@
 *.py[cod]
+*.ipynb
+.ipynb_checkpoints
 
 # C extensions
 *.so

HISTORY.rst

@@ -3,6 +3,11 @@
 History
 -------
 
+0.2.9 (10/01/2019)
+~~~~~~~~~~~~~~~~~~
+
+* Fixed error of not setting correct header information in B/SAM.
+
 0.2.8 (09/23/2019)
 ~~~~~~~~~~~~~~~~~~
 

g2gtools/__init__.py

@@ -1,3 +1,3 @@
-__version__ = '0.2.8'
+__version__ = '0.2.9'
 __author__ = 'Matthew Vincent and Kwangbom \"KB\" Choi, The Jackson Laboratory'
 __email__ = '[email protected]'

g2gtools/bsam.py

@@ -156,13 +156,12 @@ def convert_bam_file(vci_file, file_in, file_out, reverse=False):
     name_to_id = {}
     id = 0
 
-    # TODO: Fix
-    #for ref_name in sorted(chain_file.chrom_size_to):
-    #    tmp.append({'LN': chain_file.chrom_size_from[ref_name], 'SN': ref_name})
-    #    name_to_id[ref_name] = id
-    #    id += 1
+    for ref_name in vci_file.contigs:
+        tmp.append({'LN': vci_file.contigs[ref_name], 'SN': ref_name})
+        name_to_id[ref_name] = sam_file.get_tid(ref_name)
+        id += 1
 
-    #new_header['SQ'] = tmp
+    new_header['SQ'] = tmp
 
     if 'PG' not in new_header:
         new_header['PG'] = []
@@ -309,6 +308,7 @@ def convert_bam_file(vci_file, file_in, file_out, reverse=False):
 
                 mappings = vci_file.find_mappings(read_chr, read_start, read_end)
 
+
                 # unmapped
                 if mappings is None:
                     LOG.debug("\tFail due to no mappings")

setup.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 0.2.8
+current_version = 0.2.9
 commit = True
 tag = True
 

setup.py

@@ -30,7 +30,7 @@
 
 setup(
     name='g2gtools',
-    version='0.2.8',
+    version='0.2.9',
     description="A suite of tools for the reconstruction of personal diploid genomes and better coordinate conversion",
     long_description=readme + '\n\n' + history,
     author='Matthew J. Vincent and Kwangbom "KB" Choi, The Jackson Laboratory',