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Searched refs:shortMarker (Results 1 – 10 of 10) sorted by relevance

/dports/biology/velvet/velvet_1.2.10/contrib/MetaVelvet-v0.3.1/src/
H A Dscaffold.c231 ShortReadMarker *nodeArray, *shortMarker; in computeReadToNodeCounts() local
251 shortMarker = in computeReadToNodeCounts()
255 (shortMarker)]++; in computeReadToNodeCounts()
309 ShortReadMarker *shortMarker; in computePartialReadToNodeMapping() local
319 readIndex = getShortReadMarkerID(shortMarker); in computePartialReadToNodeMapping()
324 getShortReadMarkerPosition(shortMarker); in computePartialReadToNodeMapping()
326 getShortReadMarkerOffset(shortMarker); in computePartialReadToNodeMapping()
838 ShortReadMarker * shortMarker, in projectFromShortRead() argument
845 IDnum readIndex = getShortReadMarkerID(shortMarker); in projectFromShortRead()
934 ShortReadMarker *nodeArray, *shortMarker; in projectFromNode() local
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H A DgraphStats.c2094 ShortReadMarker *nodeArray, *shortMarker; in removeLowCoverageNodesAndDenounceDubiousReads() local
2158 shortMarker = in removeLowCoverageNodesAndDenounceDubiousReads()
2161 readID = getShortReadMarkerID(shortMarker); in removeLowCoverageNodesAndDenounceDubiousReads()
2173 shortMarker = in removeLowCoverageNodesAndDenounceDubiousReads()
2176 readID = getShortReadMarkerID(shortMarker); in removeLowCoverageNodesAndDenounceDubiousReads()
2428 ShortReadMarker *shortMarkerArray, *shortMarker; in exportAMOSContig() local
2466 shortMarker = in exportAMOSContig()
2469 exportAMOSShortMarker(outfile, shortMarker, reads, in exportAMOSContig()
2476 shortMarker = in exportAMOSContig()
2479 exportAMOSReverseShortMarker(outfile, shortMarker, in exportAMOSContig()
H A DshortReadPairs.c130 ShortReadMarker *nodeArray, *shortMarker; in detachImprobablePairs() local
146 shortMarker = in detachImprobablePairs()
149 seqID = getShortReadMarkerID(shortMarker); in detachImprobablePairs()
154 getShortReadMarkerPosition(shortMarker) > in detachImprobablePairs()
H A DcorrectedGraph.c727 ShortReadMarker *sourceArray, *shortMarker; in remapNodeMarkersOntoNeighbour() local
798 shortMarker = in remapNodeMarkersOntoNeighbour()
800 position = getShortReadMarkerPosition(shortMarker); in remapNodeMarkersOntoNeighbour()
823 setShortReadMarkerPosition(shortMarker, position); in remapNodeMarkersOntoNeighbour()
833 shortMarker = in remapNodeMarkersOntoNeighbour()
835 position = getShortReadMarkerPosition(shortMarker); in remapNodeMarkersOntoNeighbour()
862 setShortReadMarkerPosition(shortMarker, position); in remapNodeMarkersOntoNeighbour()
/dports/biology/velvet/velvet_1.2.10/contrib/MetaVelvet-1.2.01/Velvet-1.1.06/
H A Dscaffold.c358 ShortReadMarker *shortMarker; in computeReadToNodeCounts() local
362 readID = getShortReadMarkerID(shortMarker); in computeReadToNodeCounts()
433 ShortReadMarker *shortMarker; in computePartialReadToNodeMappingShort() local
441 shortMarker = getShortReadMarkerAtIndex(nodeArray, index); in computePartialReadToNodeMappingShort()
442 readIndex = getShortReadMarkerID(shortMarker); in computePartialReadToNodeMappingShort()
450 getShortReadMarkerPosition(shortMarker); in computePartialReadToNodeMappingShort()
452 getShortReadMarkerOffset(shortMarker); in computePartialReadToNodeMappingShort()
1413 ShortReadMarker * shortMarker, in projectFromShortRead() argument
1423 IDnum readIndex = getShortReadMarkerID(shortMarker); in projectFromShortRead()
1526 ShortReadMarker *nodeArray, *shortMarker; in projectFromNode() local
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H A DgraphStats.c1197 ShortReadMarker *shortMarker; in removeNodeAndDenounceDubiousReads() local
1205 shortMarker = getShortReadMarkerAtIndex(nodeArray, index); in removeNodeAndDenounceDubiousReads()
1206 readID = getShortReadMarkerID(shortMarker); in removeNodeAndDenounceDubiousReads()
1216 shortMarker = getShortReadMarkerAtIndex(nodeArray, index); in removeNodeAndDenounceDubiousReads()
1217 readID = getShortReadMarkerID(shortMarker); in removeNodeAndDenounceDubiousReads()
1570 ShortReadMarker *shortMarkerArray, *shortMarker; in exportAMOSContig() local
1608 shortMarker = in exportAMOSContig()
1611 exportAMOSShortMarker(outfile, shortMarker, reads, in exportAMOSContig()
1618 shortMarker = in exportAMOSContig()
1621 exportAMOSReverseShortMarker(outfile, shortMarker, in exportAMOSContig()
H A DcorrectedGraph.c704 ShortReadMarker *sourceArray, *shortMarker; in remapNodeMarkersOntoNeighbour() local
774 shortMarker = in remapNodeMarkersOntoNeighbour()
776 position = getShortReadMarkerPosition(shortMarker); in remapNodeMarkersOntoNeighbour()
799 setShortReadMarkerPosition(shortMarker, position); in remapNodeMarkersOntoNeighbour()
809 shortMarker = in remapNodeMarkersOntoNeighbour()
811 position = getShortReadMarkerPosition(shortMarker); in remapNodeMarkersOntoNeighbour()
838 setShortReadMarkerPosition(shortMarker, position); in remapNodeMarkersOntoNeighbour()
/dports/biology/velvet/velvet_1.2.10/src/
H A Dscaffold.c359 ShortReadMarker *shortMarker; in computeReadToNodeCounts() local
362 shortMarker = getShortReadMarkerAtIndex(nodeArray, in computeReadToNodeCounts()
364 readID = getShortReadMarkerID(shortMarker); in computeReadToNodeCounts()
438 ShortReadMarker *shortMarker; in computePartialReadToNodeMappingShort() local
447 readIndex = getShortReadMarkerID(shortMarker); in computePartialReadToNodeMappingShort()
455 getShortReadMarkerPosition(shortMarker); in computePartialReadToNodeMappingShort()
457 getShortReadMarkerOffset(shortMarker); in computePartialReadToNodeMappingShort()
1419 ShortReadMarker * shortMarker, in projectFromShortRead() argument
1429 IDnum readIndex = getShortReadMarkerID(shortMarker); in projectFromShortRead()
1532 ShortReadMarker *nodeArray, *shortMarker; in projectFromNode() local
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H A DgraphStats.c1186 ShortReadMarker *shortMarker; in removeNodeAndDenounceDubiousReads() local
1194 shortMarker = getShortReadMarkerAtIndex(nodeArray, index); in removeNodeAndDenounceDubiousReads()
1195 readID = getShortReadMarkerID(shortMarker); in removeNodeAndDenounceDubiousReads()
1205 shortMarker = getShortReadMarkerAtIndex(nodeArray, index); in removeNodeAndDenounceDubiousReads()
1206 readID = getShortReadMarkerID(shortMarker); in removeNodeAndDenounceDubiousReads()
1559 ShortReadMarker *shortMarkerArray, *shortMarker; in exportAMOSContig() local
1597 shortMarker = in exportAMOSContig()
1600 exportAMOSShortMarker(outfile, shortMarker, reads, in exportAMOSContig()
1607 shortMarker = in exportAMOSContig()
1610 exportAMOSReverseShortMarker(outfile, shortMarker, in exportAMOSContig()
H A DcorrectedGraph.c704 ShortReadMarker *sourceArray, *shortMarker; in remapNodeMarkersOntoNeighbour() local
774 shortMarker = in remapNodeMarkersOntoNeighbour()
776 position = getShortReadMarkerPosition(shortMarker); in remapNodeMarkersOntoNeighbour()
799 setShortReadMarkerPosition(shortMarker, position); in remapNodeMarkersOntoNeighbour()
809 shortMarker = in remapNodeMarkersOntoNeighbour()
811 position = getShortReadMarkerPosition(shortMarker); in remapNodeMarkersOntoNeighbour()
838 setShortReadMarkerPosition(shortMarker, position); in remapNodeMarkersOntoNeighbour()