nref,
p,
logodds,
pval,
nother,
sum(counts.values()),
duplicates_removed,
len(reads),
total]
outrows.append(row)
progress.update()
progress.done()
progress.stage('Multiple-test correction and FDR computation')
bonf = bonferroni(pvalues)
fdr = fdr(pvalues)
i = 0
pvalpos = outheaders.index('P-Value')
for r in outrows:
if len(r) > pvalpos:
if r[pvalpos] != emptysym:
r.insert(pvalpos + 1, fdr[i])
r.insert(pvalpos + 1, bonf[i])
i += 1
else:
r.insert(pvalpos + 1, emptysym)
r.insert(pvalpos + 1, emptysym)
progress.done()
for s in sorted(BadRead.allheaders):
row.append(badread[s])
outrows.append(row)
if not any:
# ["%s:%d_%s/%s"%(snpchr,snppos,ref,alt)] \
outrows.append([snpchr, snppos, ref, alt]
+ [snpextra.get(k, emptysym) for k in extrasnpheaders]
+ [0])
progress.update()
progress.done()
progress.stage('Multiple-test correction and FDR computation')
bonf = bonferroni(pvalues)
fdr = fdr(pvalues)
i = 0
pvalpos = outheaders.index('P-Value')
for r in outrows:
if len(r) > pvalpos:
if r[pvalpos] != emptysym:
r.insert(pvalpos + 1, fdr[i])
r.insert(pvalpos + 1, bonf[i])
i += 1
else:
r.insert(pvalpos + 1, emptysym)
r.insert(pvalpos + 1, emptysym)
progress.done()