v0.6.4

liguowang · Jul 12, 2022 · 8935dbe · 8935dbe
1 parent ee1d3f4
commit 8935dbe
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Showing 10 changed files with 14 additions and 7 deletions.
diff --git a/bin/CrossMap.py b/bin/CrossMap.py
@@ -29,7 +29,7 @@
 __copyright__ = "Copyleft"
 __credits__ = []
 __license__ = "GPLv2"
-__version__="0.6.3"
+__version__="0.6.4"
 __maintainer__ = "Liguo Wang"
 __email__ = "wangliguo78@gmail.com"
 __status__ = "Production"

diff --git a/build/lib/cmmodule/mapvcf.py b/build/lib/cmmodule/mapvcf.py
@@ -67,6 +67,7 @@ def crossmap_vcf_file(mapping, infile, outfile, liftoverfile, refgenome, noCompA
 	total = 0
 	fail = 0
 
+	chr_template = 'chr1' #if there is no contig field, use this chrom ID style.
 
 	for line in ireader.reader(infile):
 		if not line.strip():
@@ -139,10 +140,13 @@ def crossmap_vcf_file(mapping, infile, outfile, liftoverfile, refgenome, noCompA
 				continue
 
 			if len(a) == 2:
+
 				# update chrom
 				target_chr = str(a[1][0])	#target_chr is from chain file, could be 'chr1' or '1'
 				target_start = a[1][1]
 				target_end = a[1][2]
+				target_size = target_end - target_start
+
 				fields[0] = target_chr
 
 				# update start coordinate

diff --git a/build/lib/cmmodule/meta_data.py b/build/lib/cmmodule/meta_data.py
@@ -3,7 +3,7 @@
 __copyright__ = "Copyleft"
 __credits__ = []
 __license__ = "GPLv2"
-__version__="0.6.3"
+__version__="0.6.4"
 __maintainer__ = "Liguo Wang"
 __email__ = "wangliguo78@gmail.com"
 __status__ = "Production"
diff --git a/build/lib/cmmodule/utils.py b/build/lib/cmmodule/utils.py
@@ -173,7 +173,10 @@ def bigwigReader(infile):
 	bw = pyBigWig.open(infile)
 	chrom_sizes = bw.chroms()
 	for chr_name, chr_size in list(chrom_sizes.items()):
-		for i_st, i_end, i_score in bw.intervals(chr_name, 0, chr_size):
+		intervals = bw.intervals(chr_name, 0, chr_size)
+		if intervals is None:
+			continue
+		for i_st, i_end, i_score in intervals:
 			yield(( chr_name, i_st, i_end, i_score ))
 
 def check_bed12(bedline):

diff --git a/build/scripts-3.8/CrossMap.py b/build/scripts-3.8/CrossMap.py
@@ -29,7 +29,7 @@
 __copyright__ = "Copyleft"
 __credits__ = []
 __license__ = "GPLv2"
-__version__="0.6.3"
+__version__="0.6.4"
 __maintainer__ = "Liguo Wang"
 __email__ = "wangliguo78@gmail.com"
 __status__ = "Production"

diff --git a/docs/index.rst b/docs/index.rst
@@ -36,8 +36,8 @@ Release history
 
 **07/12/2022: Release version 0.6.4**
 
-1. Fix bug when the input bigwig file does not have coverage signal for some chromsomes. 
-2. When the input VCF file does not have CONTIG field, use long chromosmoe ID (e.g., "chr1") as default.
+1. Fix bug when the input bigwig file does not have coverage signal for some chromosomes. 
+2. When the input VCF file does not have CONTIG field, use long chromosome ID (e.g., "chr1") as default.
 
 **03/04/2022: Release version 0.6.3**
 

diff --git a/lib/CrossMap.egg-info/PKG-INFO b/lib/CrossMap.egg-info/PKG-INFO
@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: CrossMap
-Version: 0.6.3
+Version: 0.6.4
 Summary:  Lift over genomics coordinates between assemblies
 Home-page: https://crossmap.readthedocs.io/en/latest/
 Author: Liguo Wang

diff --git a/lib/cmmodule/__pycache__/mapvcf.cpython-38.pyc b/lib/cmmodule/__pycache__/mapvcf.cpython-38.pyc
diff --git a/lib/cmmodule/__pycache__/meta_data.cpython-38.pyc b/lib/cmmodule/__pycache__/meta_data.cpython-38.pyc
diff --git a/lib/cmmodule/__pycache__/utils.cpython-38.pyc b/lib/cmmodule/__pycache__/utils.cpython-38.pyc