gfa 0.6.0 → 0.6.1
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- checksums.yaml +4 -4
- data/bin/gfa-add-gaf +7 -5
- data/lib/gfa/graph.rb +1 -1
- data/lib/gfa/version.rb +1 -1
- metadata +1 -1
checksums.yaml
CHANGED
@@ -1,7 +1,7 @@
|
|
1
1
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---
|
2
2
|
SHA256:
|
3
|
-
metadata.gz:
|
4
|
-
data.tar.gz:
|
3
|
+
metadata.gz: cf18e4a80f49fc9c0ae4574c5c7bbc3c97fd41eaf5c7aff9fdd7991b7d562ccf
|
4
|
+
data.tar.gz: ac6999ffbbbeba45f9b81c6081ac16339ce4bb55502a77b116c77f91870af991
|
5
5
|
SHA512:
|
6
|
-
metadata.gz:
|
7
|
-
data.tar.gz:
|
6
|
+
metadata.gz: c8ae1b273166574d8520aa1f747ac0dbd08e8f31846754ca6c3fa7f0432d5f31583aa915fcebb04a220e90fe14aeeb4f06dec2a5c23527571c9bb337de0ef9a5
|
7
|
+
data.tar.gz: f5fce0959cace1fe961d92fab2946bf8b67571ee6ceef3cd6e7047d8c46f0855b28e6b703ffbfe327ef8d09e1174b94ee98423ae36bb858bab76615849e0bd94
|
data/bin/gfa-add-gaf
CHANGED
@@ -18,11 +18,13 @@ unless degree
|
|
18
18
|
<input-gaf> Input GAF file to read
|
19
19
|
<output> Output GFA file to write
|
20
20
|
<degree> Maximum degree of separation between the segment set in the GAF
|
21
|
-
and any other
|
22
|
-
|
23
|
-
|
24
|
-
|
25
|
-
|
21
|
+
and any other segments included in the output GFA.
|
22
|
+
- -1: include the complete original GAF without subsetting.
|
23
|
+
- 0: only segments in the GAF are included.
|
24
|
+
- 1: only the target segments in the GAF, records linking to
|
25
|
+
them, and segments linked by those records are included.
|
26
|
+
- Any integer > 1: include additional expansion rounds for
|
27
|
+
those linked segments.
|
26
28
|
<pref> A prefix to name all recorded paths
|
27
29
|
By default: Based on the GAF file name
|
28
30
|
<threads> If passed, parallelize process with these many threads
|
data/lib/gfa/graph.rb
CHANGED
@@ -146,7 +146,7 @@ class GFA
|
|
146
146
|
|
147
147
|
def internally_linking_records(segments, edges)
|
148
148
|
$stderr.puts '- Gathering internally linking records'
|
149
|
-
segments = Hash[segments.
|
149
|
+
segments = Hash[segments.map { |i| [i.name.value, true]}]
|
150
150
|
edges.select { |record| record.segment_names_a.all? { |s| segments[s] } }
|
151
151
|
end
|
152
152
|
|
data/lib/gfa/version.rb
CHANGED