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#include "pilercr.h"
static bool PileByPos(int PileIndex1, int PileIndex2)
{
return GetPile(PileIndex1).Lo < GetPile(PileIndex2).Lo;
}
bool GetArrayData(const IntVec &ArrayPileIndexes, ArrayData &AD)
{
if (ArrayPileIndexes.size() == 0)
Quit("GetArrayData, size=0");
#if TRACE
Log("\n");
Log("Array\n");
Log("=====\n");
#endif
for_CIntVec(ArrayPileIndexes, p)
AD.PileIndexes.push_back(*p);
// Sort by position
std::sort(AD.PileIndexes.begin(), AD.PileIndexes.end(), PileByPos);
SeqVect Seqs;
int Lo = -1;
int Hi = -1;
for_CIntVec(ArrayPileIndexes, p)
{
int PileIndex = *p;
Seq *s = new Seq;
PileToSeq(g_Piles, PileIndex, *s, &Lo, &Hi);
if (Seqs.size() == 0)
AD.Lo = Lo;
Seqs.push_back(s);
}
MSA Aln;
MultipleAlign(Seqs, Aln);
int StartCol;
int EndCol;
double MinCons = g_DraftMinCons;
const int SeqCount = (int) Aln.GetSeqCount();
if (SeqCount >= g_MinOneDiff)
{
double AltMinCons = ((double) (SeqCount - 1) / (double) SeqCount) - 0.1;
if (AltMinCons < MinCons)
MinCons = AltMinCons;
}
GetConsSeq(Aln, MinCons, &StartCol, &EndCol, AD.ConsSeq);
if ((int) AD.ConsSeq.Length() < g_DraftMinRepeatLength)
return false;
char Label[128];
sprintf(Label, "Cons%d", AD.Id);
AD.ConsSeq.SetName(Label);
AD.ConsSeq.SetId(0);
AD.RepeatLength = AD.ConsSeq.Length();
AD.SpacerLength = -1;
if (g_LogAlns)
{
Log("\n");
Log("Draft alignment for array %d:\n", AD.Id);
Aln.LogMe();
Log("\n");
Log("Consensus: ");
AD.ConsSeq.LogMeSeqOnly();
Log("\n");
Log("\n");
}
#if TRACE
Aln.LogMe();
AD.ConsSeq.LogMe();
Log("\n");
#endif
return true;
}
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