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- All Implemented Interfaces:
public class SyntenicAnchors
Class originally written by Baoxing Song for post-processing minimap2 alignments. It takes an input a file created by aligning with minimap2 and this command: /home/lcj34/minimap2/minimap2 -A 1 -B 1 -O 1 -E 1 -a -t 80 /workdir/lcj34/assemblies_by_chrom/p39/p39chr7.fa /workdir/lcj34/assemblies_by_chrom/b73/b73chr7anchors.fa >b37anchorsMap.sam The resulting .sam file (b37anchorsMap.sam in above query) is split to get 3 fields via grep: - refStart - asmStart - ms (DP score of the max scoring segment in the minimap alignment) longest path algorithm from here: https://www.geeksforgeeks.org/find-longest-path-directed-acyclic-graph/ The code currently has methods to run with mummer 4 coords file entries. The "score" from mummer alignments is (%id * alignment len)/100. Method getPairedSimilarFragmentsFromMummer() is written so this code may be applied to mummer4 alignment results. Similar methods may be added to create lists of PairedSimilarFragments from other aligners.
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Method Summary
Modifier and Type Method Description static void
myPairedSimilarFragmentSort(List<PairedSimilarFragment> pairedSimilarFragments, int score, int penalty, int scoreThreshold)
static List<PairedSimilarFragment>
getPairedSimilarFragmentsFromMummer(List<String> mummerAlignments)
Grab the ref and asm start/end positions, determine asm strand direction, calculate a score, and store all to a list of PairedSimilarFragments The score is calculated as: (%id * asmLen)/100 casted to int static List<PairedSimilarFragment>
longestIncreasingSubsequenceLAGAN(List<PairedSimilarFragment> pairedSimilarFragments)
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Method Detail
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myPairedSimilarFragmentSort
static void myPairedSimilarFragmentSort(List<PairedSimilarFragment> pairedSimilarFragments, int score, int penalty, int scoreThreshold)
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getPairedSimilarFragmentsFromMummer
static List<PairedSimilarFragment> getPairedSimilarFragmentsFromMummer(List<String> mummerAlignments)
Grab the ref and asm start/end positions, determine asm strand direction, calculate a score, and store all to a list of PairedSimilarFragments The score is calculated as: (%id * asmLen)/100 casted to int
- Parameters:
mummerAlignments
- List of String from a mummer coordinates file
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longestIncreasingSubsequenceLAGAN
static List<PairedSimilarFragment> longestIncreasingSubsequenceLAGAN(List<PairedSimilarFragment> pairedSimilarFragments)
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