diff --git a/pairtools/lib/dedup.py b/pairtools/lib/dedup.py index 72ebc35..f2b1506 100644 --- a/pairtools/lib/dedup.py +++ b/pairtools/lib/dedup.py @@ -4,6 +4,7 @@ import scipy.spatial from scipy.sparse import coo_matrix from scipy.sparse.csgraph import connected_components +from csv import QUOTE_NONE from . import dedup_cython, pairsam_format from .stats import PairCounter @@ -79,7 +80,7 @@ def streaming_dedup( # Stream the dups: if outstream_dups: df_chunk.loc[mask_mapped & mask_duplicates, :].to_csv( - outstream_dups, index=False, header=False, sep="\t" + outstream_dups, index=False, header=False, sep="\t", quoting=QUOTE_NONE ) # Drop readID if it was created (not needed for nodup and unmapped pairs): @@ -89,12 +90,12 @@ def streaming_dedup( # Stream unmapped: if outstream_unmapped: df_chunk.loc[~mask_mapped, :].to_csv( - outstream_unmapped, index=False, header=False, sep="\t" + outstream_unmapped, index=False, header=False, sep="\t", quoting=QUOTE_NONE ) # Stream unique pairs: df_chunk.loc[mask_mapped & (~mask_duplicates), :].to_csv( - outstream, index=False, header=False, sep="\t" + outstream, index=False, header=False, sep="\t", quoting=QUOTE_NONE ) t1 = time.time()