Fix query->target synteny navigation

plugins/alignments/src/BamAdapter/MismatchParser.ts

@@ -1,4 +1,5 @@
 import { revcom } from '@jbrowse/core/util'
+
 export interface Mismatch {
   qual?: number
   start: number
@@ -11,9 +12,12 @@ export interface Mismatch {
 }
 const mdRegex = new RegExp(/(\d+|\^[a-z]+|[a-z])/gi)
 const modificationRegex = new RegExp(/([A-Z])([-+])([^,.?]+)([.?])?/)
+const cigarRegex = new RegExp(/([MIDNSHPX=])/)
+
 export function parseCigar(cigar = '') {
-  return cigar.split(/([MIDNSHPX=])/).slice(0, -1)
+  return cigar.split(cigarRegex).slice(0, -1)
 }
+
 export function cigarToMismatches(
   ops: string[],
   seq?: string,
@@ -339,3 +343,47 @@ export function getModificationTypes(mm: string) {
     })
     .flat()
 }
+
+export function getOrientedCigar(flip: boolean, cigar: string[]) {
+  if (flip) {
+    const ret = []
+    for (let i = 0; i < cigar.length; i += 2) {
+      const len = cigar[i]
+      let op = cigar[i + 1]
+      if (op === 'D') {
+        op = 'I'
+      } else if (op === 'I') {
+        op = 'D'
+      }
+      ret.push(len)
+      ret.push(op)
+    }
+    return ret
+  } else {
+    return cigar
+  }
+}
+
+export function getOrientedMismatches(flip: boolean, cigar: string) {
+  const mismatches = getMismatches(cigar)
+  if (flip) {
+    let startReadjuster = 0
+    return mismatches.map(m => {
+      if (m.type === 'insertion') {
+        m.type = 'deletion'
+        m.length = +m.base
+        m.start += startReadjuster
+        startReadjuster += m.length
+      } else if (m.type === 'deletion') {
+        const len = m.length
+        m.type = 'insertion'
+        m.base = `${len}`
+        m.length = 0
+        m.start += startReadjuster
+        startReadjuster -= len
+      }
+      return m
+    })
+  }
+  return mismatches
+}

plugins/comparative-adapters/src/PAFAdapter/PAFAdapter.ts

@@ -16,7 +16,7 @@ import { MismatchParser } from '@jbrowse/plugin-alignments'
 
 // locals
 import { zip, isGzip } from '../util'
-const { getMismatches } = MismatchParser
+const { getOrientedMismatches } = MismatchParser
 
 export interface PAFRecord {
   qname: string
@@ -131,30 +131,6 @@ function weightedMean(tuples: [number, number][]) {
   return valueSum / weightSum
 }
 
-function getOrientedMismatches(flip: boolean, cigar: string) {
-  const mismatches = getMismatches(cigar)
-  if (flip) {
-    let startReadjuster = 0
-    return mismatches.map(m => {
-      if (m.type === 'insertion') {
-        m.type = 'deletion'
-        m.length = +m.base
-        m.start += startReadjuster
-        startReadjuster += m.length
-      } else if (m.type === 'deletion') {
-        const len = m.length
-        m.type = 'insertion'
-        m.base = `${len}`
-        m.length = 0
-        m.start += startReadjuster
-        startReadjuster -= len
-      }
-      return m
-    })
-  }
-  return mismatches
-}
-
 class SyntenyFeature extends SimpleFeature {
   // eslint-disable-next-line @typescript-eslint/no-explicit-any
   get(arg: string): any {
@@ -332,13 +308,13 @@ export default class PAFAdapter extends BaseFeatureDataAdapter {
               end,
               type: 'match',
               refName,
-              strand, // : !flip ? strand * -1 : strand,
+              strand,
 
               // this is a special property of how to interpret CIGAR on PAF,
-              // intrinsic to the data format. the CIGAR is read backwards
-              // for features aligning to the negative strand of the target,
-              // which is actually different than how it works in e.g.
-              // BAM/SAM (which is visible during alignments track read vs ref)
+              // intrinsic to the data format. the CIGAR is read backwards for
+              // features aligning to the negative strand of the target, which
+              // is actually different than how it works in e.g. BAM/SAM (which
+              // is visible during alignments track read vs ref)
               revCigar: true,
 
               // depending on whether the query or target is queried, the

plugins/linear-comparative-view/src/LGVSyntenyDisplay/stateModelFactory.ts

@@ -20,12 +20,13 @@ import { LinearSyntenyViewModel } from '../LinearSyntenyView/model'
 
 type LSV = LinearSyntenyViewModel
 
-const { parseCigar } = MismatchParser
+const { parseCigar, getOrientedCigar } = MismatchParser
 
-function findPosInCigar(cigar: string[], x: number) {
+function findPosInCigar(inCigar: string[], flip: boolean, x: number) {
   let featX = 0
   let mateX = 0
-  for (let i = 0; i < cigar.length; i += 2) {
+  const cigar = getOrientedCigar(flip, inCigar)
+  for (let i = 0; i < cigar.length; i++) {
     const len = +cigar[i]
     const op = cigar[i + 1]
     const min = Math.min(len, x - featX)
@@ -57,6 +58,7 @@ async function navToSynteny(feature: Feature, self: any) {
   const featStart = feature.get('start')
   const featEnd = feature.get('end')
   const mate = feature.get('mate')
+  const flip = feature.get('flipInsDel')
   const mateStart = mate.start
   const mateEnd = mate.end
   const mateAsm = mate.assemblyName
@@ -69,16 +71,16 @@ async function navToSynteny(feature: Feature, self: any) {
   let rFeatStart = featStart
   let rFeatEnd = featStart
 
-  if (cigar.length) {
-    const [featStartX, mateStartX] = findPosInCigar(cigar, regStart - featStart)
-    const [featEndX, mateEndX] = findPosInCigar(cigar, regEnd - featStart)
+  if (cigar) {
+    const [fStartX, mStartX] = findPosInCigar(cigar, flip, regStart - featStart)
+    const [fEndX, mEndX] = findPosInCigar(cigar, flip, regEnd - featStart)
 
     // avoid multiply by 0 with strand undefined
     const flipper = strand === -1 ? -1 : 1
-    rFeatStart = featStart + featStartX
-    rFeatEnd = featStart + featEndX
-    rMateStart = mateStart + mateStartX * flipper
-    rMateEnd = mateStart + mateEndX * flipper
+    rFeatStart = featStart + fStartX
+    rFeatEnd = featStart + fEndX
+    rMateStart = mateStart + mStartX * flipper
+    rMateEnd = mateStart + mEndX * flipper
   } else {
     rFeatEnd = featEnd
     rMateEnd = mateEnd