int main(int argv, char *argc[])
{
FILE *fp, *fp2;
fp=fopen(argc[1],"r");
fp2=fopen(argc[2],"r");
readClones(fp);
// printf("L94\n");
readAlignments(fp2);
// printf("L96\n");
outputTheReads();
}
void ppAnalyse(char *headersName, char *sizesName, char *pairsPsl,
char *finDir, char *pairOut, char *mispairOut)
/* ppAnalyse - Analyse paired plasmid reads. */
{
struct hash *readHash = newHash(21);
struct hash *pairHash = newHash(20);
struct hash *fragHash = newHash(17);
struct hash *finHash = NULL;
struct hash *gsiHash = newHash(8);
struct pairInfo *pairList = NULL, *measuredList, *pair;
struct readInfo *readList = NULL, *rd;
struct groupSizeInfo *gsiList = NULL, *gsi;
int aliCount;
int finCount;
int i;
struct slName *finList, *name;
finHash = newHash(14);
finList = listDir(finDir, "*.fa");
if ((finCount = slCount(finList)) == 0)
errAbort("No fa files in %s\n", finDir);
printf("Got %d (finished) .fa files in %s\n", finCount, finDir);
for (name = finList; name != NULL; name = name->next)
{
chopSuffix(name->name);
hashStore(finHash, name->name);
}
#ifdef SOMETIMES
#endif /* SOMETIMES */
gsiList = readSizes(sizesName, gsiHash);
printf("Got %d groups\n", slCount(gsiList));
readHeaders(headersName, readHash, pairHash, &readList, &pairList);
slReverse(&readList);
slReverse(&pairList);
printf("Got %d reads in %d pairs\n", slCount(readList), slCount(pairList));
savePairs(pairOut, pairList, gsiHash);
printf("Saved pairs to %s\n", pairOut);
aliCount = readAlignments(pairsPsl, readHash, fragHash);
printf("Got %d alignments in %s\n", aliCount, pairsPsl);
doReadStats(readList, aliCount);
doPairStats(pairList, finHash, gsiHash, mispairOut, &measuredList, &pairList);
gsiMeanAndVariance(measuredList, gsiList, gsiHash, finHash);
printf("Alignment length stats:\n");
for (i=0; i<10; ++i)
{
printf("%3d - %4d : %6d %4.2f%%\n",
i*100, (i+1)*100, aliSizes[i], 100.0 * (double)aliSizes[i]/(double)aliCount);
}
doMeasuredStats(measuredList);
for (gsi = gsiList; gsi != NULL; gsi = gsi->next)
{
if (gsi->measuredCount > 0)
{
printf("%s: mean %f, std %f, min %d, max %d, samples %d\n",
gsi->name, gsi->measuredMean, sqrt(gsi->variance),
gsi->measuredMin, gsi->measuredMax,
gsi->measuredCount);
printf(" %4.2f%% within guessed range (%d-%d)\n",
100.0 * (double)gsi->guessedCount/(double)gsi->measuredCount,
gsi->guessedMin, gsi->guessedMax);
printf(" w/in 200 %4.2f%%, w/in 400 %4.2f%%, w/in 800 %4.2f%%, w/in 1600 %4.3f%%, w/in 3200 %4.2f%%\n\n",
gsiTight(gsi, 200), gsiTight(gsi, 400), gsiTight(gsi, 800), gsiTight(gsi, 1600), gsiTight(gsi, 3200) );
showHistogram(gsi);
}
}
}