Merge pull request #333 from fransua/master

faster parsing

Author: david-castillo

_pytadbit/parsers/hic_bam_parser.py

@@ -374,13 +374,6 @@ def _read_bam_frag(inbam, filter_exclude, all_bins, sections1, sections2,
     refs = bamfile.references
     bam_start = start - 2
     bam_start = max(0, bam_start)
-    section_pos = []
-    for sec in sections1:
-        if sec not in section_pos:
-            section_pos.append(sec[0])
-    for sec in sections2:
-        if sec not in section_pos:
-            section_pos.append(sec[0])
     try:
         dico = {}
         for r in bamfile.fetch(region=region,
@@ -677,7 +670,7 @@ def read_bam(inbam, filter_exclude, resolution, ncpus=8,
         if ncpus == 1:
             read_bam_frag(inbam, filter_exclude, all_bins,
                           bins_dict1, bins_dict2, rand_hash,
-                          resolution, tmpdir, region, b, e,)
+                          resolution, tmpdir, region, b, e)
         else:
             procs.append(pool.apply_async(
                 read_bam_frag, args=(inbam, filter_exclude, all_bins,

_pytadbit/parsers/sam_parser.py

@@ -108,7 +108,7 @@ def parse_sam(f_names1, f_names2=None, out_file1=None, out_file2=None,
             if mapper.lower()=='gem':
                 condition = lambda x: x[1][0][0] != 'N'
             elif mapper.lower() in ['bowtie', 'bowtie2']:
-                condition = lambda x: 'XS' in dict(x)
+                condition = lambda x: 'XS' == x[0][0]
             else:
                 warn('WARNING: unrecognized mapper used to generate file\n')
                 condition = lambda x: x[1][1] != 1