diff --git a/docs/caller_usage.md b/docs/caller_usage.md index d1c647f..3f2bfaa 100644 --- a/docs/caller_usage.md +++ b/docs/caller_usage.md @@ -17,7 +17,7 @@ from 0.0-0.4. **Default:** 0.9 * `--max-rcn-iters ##`: Maximum number of read copy-number counting iterations to perform. Loci which require a lot of iterations are probably impure tandem repeats, for which the resulting copy number will not be very accurate anyway. - **Default:** 200 + **Default:** 50 * `--flank-size ##`: Size of the flanking region to use on either side of a region to properly anchor reads. **Default:** 70 * `--realign` or `-a`: Whether to perform local re-alignment to attempt recovery of soft-clipped reads. Some aligners diff --git a/strkit/call/params.py b/strkit/call/params.py index 7dbb390..4842313 100644 --- a/strkit/call/params.py +++ b/strkit/call/params.py @@ -23,7 +23,7 @@ def __init__( max_reads: int = 250, min_avg_phred: int = 13, min_read_align_score: float = 0.9, - max_rcn_iters: int = 200, + max_rcn_iters: int = 50, num_bootstrap: int = 100, flank_size: int = 70, skip_supplementary: bool = False, diff --git a/strkit/entry.py b/strkit/entry.py index 7a31d00..0b08781 100644 --- a/strkit/entry.py +++ b/strkit/entry.py @@ -134,7 +134,7 @@ def add_call_parser_args(call_parser): call_parser.add_argument( "--max-rcn-iters", "--mrci", type=int, - default=200, + default=50, help=( "Maximum number of read copy-number counting iterations to perform. Loci which require a lot of " "iterations are probably impure tandem repeats, for which the resulting copy number will not be very "