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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,55 @@ | ||
| #include <stdio.h> | ||
| #include <stdlib.h> | ||
| #include <string.h> | ||
| #include <zlib.h> | ||
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|
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| #define MAX_LINE 1000000 | ||
| #define NUM_BINS 16 | ||
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| // Function to determine the bin for a given length | ||
| int get_bin(int length) { | ||
| int bins[] = {10, 100, 1000, 2500, 5000, 10000, 20000, 35000, 50000, 75000, 100000, 200000, 300000, 500000, 750000, 1000000}; | ||
| for (int i = 0; i < NUM_BINS; i++) { | ||
| if (length <= bins[i]) { | ||
| return i; | ||
| } | ||
| } | ||
| return NUM_BINS - 1; // For reads longer than the last bin | ||
| } | ||
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| int main(int argc, char *argv[]) { | ||
| if (argc != 2) { | ||
| fprintf(stderr, "Usage: %s <fastq_file>\n", argv[0]); | ||
| return 1; | ||
| } | ||
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| gzFile fp = gzopen(argv[1], "r"); | ||
| if (!fp) { | ||
| fprintf(stderr, "Error: Could not open file %s\n", argv[1]); | ||
| return 1; | ||
| } | ||
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| char line[MAX_LINE]; | ||
| int counters[NUM_BINS] = {0}; | ||
| int line_count = 0; | ||
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| while (gzgets(fp, line, sizeof(line))) { | ||
| line_count++; | ||
| if (line_count % 4 == 2) { // This is the sequence line | ||
| int length = strlen(line) - 1; // Subtract 1 to remove newline | ||
| int bin = get_bin(length); | ||
| counters[bin]++; | ||
| } | ||
| } | ||
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| gzclose(fp); | ||
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| // Print results | ||
| printf("Bin,Number of Reads\n"); | ||
| int bins[] = {10, 100, 1000, 2500, 5000, 10000, 20000, 35000, 50000, 75000, 100000, 200000, 300000, 500000, 750000, 1000000}; | ||
| for (int i = 0; i < NUM_BINS; i++) { | ||
| printf("%d,%d\n", bins[i], counters[i]); | ||
| } | ||
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||
| return 0; | ||
| } |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,34 @@ | ||
| #!/bin/bash | ||
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||
| # Check if required arguments are provided | ||
| if [ "$#" -lt 3 ]; then | ||
| echo "Usage: $0 <input_file> <FORMAT> <OUTDIR>" | ||
| exit 1 | ||
| fi | ||
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| INPUT_FILE=$1 | ||
| FORMAT=$2 | ||
| OUTDIR=$3 | ||
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| # Process the input file and generate the string | ||
| GENERATED_STRING=$(awk -F',' ' | ||
| NR>1 { | ||
| if ($1 ~ /^[0-9]+$/ && $2 ~ /^[0-9]+$/ && $2 > 0) { | ||
| printf "%d*%d ", $2, $1 | ||
| } | ||
| } | ||
| ' "$INPUT_FILE" | sed 's/ $//') | ||
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| # Run the n50_simreads command with the generated string | ||
| n50_simreads --${FORMAT} -o ${OUTDIR} $GENERATED_STRING | ||
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| # Print the command that was executed (for verification) | ||
| echo "Executed command: n50_simreads --${FORMAT} -o ${OUTDIR} $GENERATED_STRING" | ||
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| # Calculate and print total number of reads | ||
| TOTAL_READS=$(awk -F',' 'NR>1 && $2 ~ /^[0-9]+$/ {sum += $2} END {print sum}' "$INPUT_FILE") | ||
| echo "Total number of reads: $TOTAL_READS" | ||
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| # Find the maximum read length | ||
| MAX_LENGTH=$(awk -F',' 'NR>1 && $1 ~ /^[0-9]+$/ && $2 > 0 {max=$1} END {print max}' "$INPUT_FILE") | ||
| echo "Maximum read length: $MAX_LENGTH" |