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Work-around for lumpy segfaults from lumpyexpress #277

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Work-around for lumpy segfaults from lumpyexpress #277

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The call to lumpy from lumpyexpress segfaults when the -pe flags are …
hepcat72 Oct 18, 2018
6df60a0
Changes to get around errors in some cases
hepcat72 Mar 26, 2019
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9 changes: 3 additions & 6 deletions scripts/lumpyexpress
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Original file line number Diff line number Diff line change
Expand Up @@ -183,7 +183,7 @@ do
x)
EXCLUDE_BED="$OPTARG"
EXCLUDE_BED_FMT="-x $EXCLUDE_BED"
;;
;;
T)
TEMP_DIR="$OPTARG"
;;
Expand Down Expand Up @@ -438,7 +438,7 @@ then
mv ${TEMP_DIR}/$OUTBASE.sample$(($i+1)).lib$(($j+1)).discordants.bam ${TEMP_DIR}/$OUTBASE.sample$(($i+1)).discordants.bam
mv ${TEMP_DIR}/$OUTBASE.sample$(($i+1)).lib$(($j+1)).splitters.bam ${TEMP_DIR}/$OUTBASE.sample$(($i+1)).splitters.bam
fi

# update the splitters and discordant BAM lists
SPL_BAM_LIST+=(${TEMP_DIR}/$OUTBASE.sample$(($i+1)).splitters.bam)
DISC_BAM_LIST+=(${TEMP_DIR}/$OUTBASE.sample$(($i+1)).discordants.bam)
Expand Down Expand Up @@ -500,10 +500,7 @@ else
STDEV=`cat ${TEMP_DIR}/$OUTBASE.sample$(($i+1)).lib$(($j+1)).insert.stats | tr '\t' '\n' | grep "^stdev" | sed 's/stdev\://g'`
RG_STRING=`echo "${LIB_RG_LIST[$j]}" | sed 's/,/,read_group:/g' | sed 's/^/read_group:/g'`

if [[ "$MEAN" != "NA" ]] && [[ "$STDEV" != "NA" ]]
then
LUMPY_DISC_STRING="$LUMPY_DISC_STRING -pe bam_file:${DISC_BAM},histo_file:${TEMP_DIR}/$OUTBASE.sample$(($i+1)).lib$(($j+1)).x4.histo,mean:${MEAN},stdev:${STDEV},read_length:${LIB_READ_LENGTH_LIST[$j]},min_non_overlap:${LIB_READ_LENGTH_LIST[$j]},discordant_z:5,back_distance:10,weight:1,id:${DISC_SAMPLE},min_mapping_threshold:20,${RG_STRING}"
fi
LUMPY_DISC_STRING="$LUMPY_DISC_STRING -pe bam_file:${DISC_BAM},histo_file:${TEMP_DIR}/$OUTBASE.sample$(($i+1)).lib$(($j+1)).x4.histo,mean:${MEAN},stdev:${STDEV},read_length:${LIB_READ_LENGTH_LIST[$j]},min_non_overlap:${LIB_READ_LENGTH_LIST[$j]},discordant_z:5,back_distance:10,weight:1,id:${DISC_SAMPLE},min_mapping_threshold:20,${RG_STRING}"
done
done
fi
Expand Down
35 changes: 16 additions & 19 deletions scripts/pairend_distro.py
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Original file line number Diff line number Diff line change
Expand Up @@ -112,22 +112,22 @@ def mean_std(L):
min_elements = 1000
if len(L) < min_elements:
sys.stderr.write("Warning: only %s elements in distribution (min: %s)\n" % (len(L), min_elements))
mean = "NA"
stdev = "NA"

else:
# Remove outliers
med, umad = unscaled_upper_mad(L)
upper_cutoff = med + options.mads * umad
L = [v for v in L if v < upper_cutoff]
new_len = len(L)
removed = c - new_len
sys.stderr.write("Removed %d outliers with isize >= %d\n" %
(removed, upper_cutoff))
c = new_len

mean, stdev = mean_std(L)

# Remove outliers
med, umad = unscaled_upper_mad(L)
upper_cutoff = med + options.mads * umad
L = [v for v in L if v < upper_cutoff]
new_len = len(L)
removed = c - new_len
sys.stderr.write("Removed %s outliers with isize >= %s\n" %
(removed, upper_cutoff))
c = new_len

mean, stdev = mean_std(L)

f = open(options.output_file, 'w')

if not np.isnan(mean) and not np.isnan(stdev):
start = options.read_length
end = int(mean + options.X*stdev)

Expand All @@ -140,13 +140,10 @@ def mean_std(L):
H[j] = H[ int(x - start) ] + 1
s += 1

f = open(options.output_file, 'w')

for i in range(end - start):
o = str(i) + "\t" + str(float(H[i])/float(s)) + "\n"
f.write(o)


f.close()
f.close()

print(('mean:' + str(mean) + '\tstdev:' + str(stdev)))