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1 #!/bin/bash
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2 #get_average_contig_coverage $perc $contig $bam
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3 #returns "1" -> #low coverage, "0" -> #in tolerance
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4 perc=$1; contig=$2; bam=$3; reference=$4;
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5
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6 pro_coverage=`samtools mpileup -f $reference -r $contig $bam | cut -f 4 | awk '{s+=$1}END{print s}' 2>/dev/null`;
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7
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8 if [ -z "$pro_coverage" ]; then
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9 coverage=0;
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10 else
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11 coverage=$pro_coverage;
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12 fi
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13
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14 pro_positions=`samtools mpileup -f $reference -r $contig $bam | wc -l 2>/dev/null`
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15
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16 if [ -z "$pro_positions" ]; then
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17 positions=0;
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18 else
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19 positions=$pro_positions;
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20 fi
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21
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22 if [[ $positions -eq $zero ]]; then
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23 echo "1";
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24 exit;
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25 fi
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26
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27
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28 average_coverage=`echo "scale=3; $coverage/$positions" | bc`;
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29
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30 if (( $(echo "$average_coverage < $perc"|bc -l) )); then
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31 echo "1"; #low coverage
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32 else
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33 echo "0"; #in tolerance
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34 fi
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