Enable selective alignment and gcBias flags

Novartis · Jul 9, 2021 · f0a0f0f · f0a0f0f
1 parent 89093de
commit f0a0f0f
Showing 1 changed file with 2 additions and 2 deletions.
diff --git a/pisces/__init__.py b/pisces/__init__.py
@@ -271,15 +271,15 @@ def format_salmon_command(libtype, threads, index, output_dir, read1, read2,
                          'bin', 'salmon'), '--no-version-check', 'quant', '-q',
             '--index', index, '--libType', libtype, '--mates1', ' '.join(read1),
             '--mates2', ' '.join(read2), '--output', output_dir, '--threads',
-            str(threads), '--seqBias', '--useVBOpt'
+            str(threads), '--seqBias', '--gcBias', '--validateMappings', '--dumpEq'
         ]
     elif not read2:
         cmd = [
             os.path.join(data_dir, 'redist', 'salmon',
                          'bin', 'salmon'), '--no-version-check', 'quant', '-q',
             '--index', index, '--libType', libtype, '-r', ' '.join(read1), '--output',
             output_dir, '--threads',
-            str(threads), '--seqBias', '--useVBOpt'
+            str(threads), '--seqBias', '--gcBias', '--validateMappings', '--dumpEq'
         ]
     if make_bam:
         import shlex