SyntenicAnchors

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.

Nested Class Summary

Nested Classes
Modifier and Type	Class	Description

Field Summary

Fields
Modifier and Type	Field	Description

Constructor Summary

Constructors
Constructor	Description

Enum Constant Summary

Enum Constants
Enum Constant	Description

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)`

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

- Constructor Detail
- Method Detail
  - myPairedSimilarFragmentSort
```
 static void myPairedSimilarFragmentSort(List<PairedSimilarFragment> pairedSimilarFragments, int score, int penalty, int scoreThreshold)
```
  - 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
  - longestIncreasingSubsequenceLAGAN
```
 static List<PairedSimilarFragment> longestIncreasingSubsequenceLAGAN(List<PairedSimilarFragment> pairedSimilarFragments)
```