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augur/frequencies: fix determination of interval for clipping of non-…

…informative pivots and set to 2y
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rneher committed Sep 18, 2019
1 parent ffb929a commit f7f0e57e63590539836fb9b27d4fc59287c00310
Showing with 2 additions and 2 deletions.
  1. +1 −1 augur/frequencies.py
  2. +1 −1 augur/frequency_estimators.py
@@ -205,7 +205,7 @@ def run(args):
position, state = mutation.split(":")
frequencies["%s:%s%s" % (gene, position, state)] = format_frequencies(mutation_frequencies)
else:
freqs = alignment_frequencies(aln, tps, pivots, stiffness=stiffness, inertia=inertia, method='SLSQP')
freqs = alignment_frequencies(aln, tps, pivots, stiffness=stiffness, inertia=inertia, method='SLSQP', dtps=2.0)
freqs.mutation_frequencies(min_freq = args.minimal_frequency, ignore_char=args.ignore_char)
frequencies.update({"%s:%d%s" % (gene, pos+1, state): format_frequencies(mutation_frequencies)
for (pos, state), mutation_frequencies in freqs.frequencies.items()})
@@ -328,7 +328,7 @@ def __init__(self, tps, obs, pivots, dtps=None, **kwargs):
if dtps==None:
self.dtps = 6.0*pivot_dt
else:
self.dtps = np.max(dtps, pivot_dt)
self.dtps = max(dtps, pivot_dt)

cum_obs = np.diff(self.obs).cumsum()
first_obs = max(pivots[0], self.tps[cum_obs.searchsorted(cum_obs[0]+1)])

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