@jbrowse/cli 5.0.0-beta.1 → 5.0.0-beta.11

package/dist/commands/make-pif/cigar-utils.js

@@ -1,67 +0,0 @@
-// Walk a CIGAR and split the alignment wherever an insertion or deletion is at
-// least `splitGap` bp, so each coarse-tier row's bounding box stays tight.
-// Returns one segment per contiguous run; `splitGap` must be positive (the
-// caller keeps the whole row when there is nothing to split on).
-// PAF semantics: qstart < qend always; '-' strand CIGAR walks query backward.
-export function splitCigarOnLargeGaps({ cigar, strand, tstart, tend, qstart, qend, splitGap, }) {
-    const qStep = strand === '-' ? -1 : 1;
-    let tCursor = tstart;
-    let qCursor = strand === '-' ? qend : qstart;
-    let segTStart = tCursor;
-    let segQAnchor = qCursor;
-    let segBlockLen = 0;
-    const out = [];
-    const emit = () => {
-        if (tCursor > segTStart || qCursor !== segQAnchor) {
-            out.push({
-                tstart: segTStart,
-                tend: tCursor,
-                qstart: Math.min(segQAnchor, qCursor),
-                qend: Math.max(segQAnchor, qCursor),
-                blockLen: segBlockLen,
-            });
-        }
-    };
-    // Parse CIGAR directly to avoid intermediate array + string-to-number conversions
-    let i = 0;
-    while (i < cigar.length) {
-        let len = 0;
-        while (i < cigar.length &&
-            cigar.charCodeAt(i) >= 48 &&
-            cigar.charCodeAt(i) <= 57) {
-            len = len * 10 + cigar.charCodeAt(i++) - 48;
-        }
-        const op = cigar[i++];
-        if ('M=X'.includes(op)) {
-            tCursor += len;
-            qCursor += len * qStep;
-            segBlockLen += len;
-        }
-        else if ('DIN'.includes(op)) {
-            const isLarge = len >= splitGap;
-            if (isLarge) {
-                emit();
-            }
-            if (op === 'I') {
-                qCursor += len * qStep;
-            }
-            else {
-                tCursor += len;
-            }
-            if (isLarge) {
-                segTStart = tCursor;
-                segQAnchor = qCursor;
-                segBlockLen = 0;
-            }
-            else {
-                segBlockLen += len;
-            }
-        }
-        // S/H/P (clipping/padding) don't consume target or forward-strand query in PAF
-    }
-    emit();
-    return {
-        segments: out,
-        closed: tCursor === tend && qCursor === (strand === '-' ? qstart : qend),
-    };
-}