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distinguish query and reference thresholds
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introduce query/reference overlap/gap thresholds
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David Heller committed Sep 11, 2019
1 parent ad046de commit e9a2f68
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Showing 2 changed files with 107 additions and 60 deletions.
72 changes: 56 additions & 16 deletions src/svim_asm/SVIM_input_parsing.py
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Original file line number Diff line number Diff line change
Expand Up @@ -59,24 +59,44 @@ def parse_arguments(program_version, arguments = sys.argv[1:]):
indicate a very long deletion (inversion) or a translocation breakpoint. \
SVIM calls a translocation breakpoint if the mapping distance is larger \
than this parameter and a deletion (or inversion) if it is smaller or equal.')
group_haploid_collect.add_argument('--segment_gap_tolerance',
group_haploid_collect.add_argument('--query_gap_tolerance',
type=int,
default=50,
help='Maximum tolerated gap between adjacent alignment segments (default: %(default)s). \
This parameter applies to gaps on the reference and the query. Example: \
help='Maximum tolerated gap between adjacent alignment segments on the query \
(default: %(default)s). Example: \
Deletions are detected from two subsequent segments of a split query sequence that are mapped \
far apart from each other on the reference. The segment gap tolerance determines \
far apart from each other on the reference. The query gap tolerance determines \
the maximum tolerated length of the query gap between both segments. If there is an \
unaligned query segment larger than this value between the two segments, no deletion is called.')
group_haploid_collect.add_argument('--segment_overlap_tolerance',
group_haploid_collect.add_argument('--query_overlap_tolerance',
type=int,
default=50,
help='Maximum tolerated overlap between adjacent alignment segments (default: %(default)s). \
This parameter applies to overlaps on the reference and the query. Example: \
help='Maximum tolerated overlap between adjacent alignment segments on the query \
(default: %(default)s). Example: \
Deletions are detected from two subsequent segments of a split query sequence that are mapped \
far apart from each other on the reference. The segment overlap tolerance determines \
far apart from each other on the reference. The query overlap tolerance determines \
the maximum tolerated length of an overlap between both segments in the query. If the \
overlap between the two segments in the query is larger than this value, no deletion is called.')
group_haploid_collect.add_argument('--reference_gap_tolerance',
type=int,
default=50,
help='Maximum tolerated gap between adjacent alignment segments on the reference \
(default: %(default)s). Example: \
Insertions are detected from two segments of a split query sequence that are mapped \
right next to each other on the reference but with unaligned sequence between them on the query. \
The reference gap tolerance determines the maximum tolerated length of the reference gap between \
both segments. If there is a reference gap larger than this value between the two segments, no \
insertion is called.')
group_haploid_collect.add_argument('--reference_overlap_tolerance',
type=int,
default=50,
help='Maximum tolerated overlap between adjacent alignment segments on the reference \
(default: %(default)s). Example: \
Insertions are detected from two segments of a split query sequence that are mapped \
right next to each other on the reference but with unaligned sequence between them on the query. \
The reference overlap tolerance determines the maximum tolerated length of an overlap between \
both segments on the reference. If there is a reference gap larger than this value between the \
two segments, no insertion is called.')

group_haploid_output = parser_haploid.add_argument_group('OUTPUT')
group_haploid_output.add_argument('--sample',
Expand Down Expand Up @@ -144,24 +164,44 @@ def parse_arguments(program_version, arguments = sys.argv[1:]):
indicate a very long deletion (inversion) or a translocation breakpoint. \
SVIM calls a translocation breakpoint if the mapping distance is larger \
than this parameter and a deletion (or inversion) if it is smaller or equal.')
group_diploid_collect.add_argument('--segment_gap_tolerance',
group_diploid_collect.add_argument('--query_gap_tolerance',
type=int,
default=50,
help='Maximum tolerated gap between adjacent alignment segments (default: %(default)s). \
This parameter applies to gaps on the reference and the query. Example: \
help='Maximum tolerated gap between adjacent alignment segments on the query \
(default: %(default)s). Example: \
Deletions are detected from two subsequent segments of a split query sequence that are mapped \
far apart from each other on the reference. The segment gap tolerance determines \
far apart from each other on the reference. The query gap tolerance determines \
the maximum tolerated length of the query gap between both segments. If there is an \
unaligned query segment larger than this value between the two segments, no deletion is called.')
group_diploid_collect.add_argument('--segment_overlap_tolerance',
group_diploid_collect.add_argument('--query_overlap_tolerance',
type=int,
default=50,
help='Maximum tolerated overlap between adjacent alignment segments (default: %(default)s). \
This parameter applies to overlaps on the reference and the query. Example: \
help='Maximum tolerated overlap between adjacent alignment segments on the query \
(default: %(default)s). Example: \
Deletions are detected from two subsequent segments of a split query sequence that are mapped \
far apart from each other on the reference. The segment overlap tolerance determines \
far apart from each other on the reference. The query overlap tolerance determines \
the maximum tolerated length of an overlap between both segments in the query. If the \
overlap between the two segments in the query is larger than this value, no deletion is called.')
group_diploid_collect.add_argument('--reference_gap_tolerance',
type=int,
default=50,
help='Maximum tolerated gap between adjacent alignment segments on the reference \
(default: %(default)s). Example: \
Insertions are detected from two segments of a split query sequence that are mapped \
right next to each other on the reference but with unaligned sequence between them on the query. \
The reference gap tolerance determines the maximum tolerated length of the reference gap between \
both segments. If there is a reference gap larger than this value between the two segments, no \
insertion is called.')
group_diploid_collect.add_argument('--reference_overlap_tolerance',
type=int,
default=50,
help='Maximum tolerated overlap between adjacent alignment segments on the reference \
(default: %(default)s). Example: \
Insertions are detected from two segments of a split query sequence that are mapped \
right next to each other on the reference but with unaligned sequence between them on the query. \
The reference overlap tolerance determines the maximum tolerated length of an overlap between \
both segments on the reference. If there is a reference gap larger than this value between the \
two segments, no insertion is called.')

group_diploid_pair = parser_diploid.add_argument_group('PAIR')
group_diploid_pair.add_argument('--max_edit_distance',
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