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1 #include <assert.h>
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2 #include <ctype.h>
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3 #include <stdlib.h>
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4 #include <zlib.h>
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5 #include <stdio.h>
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6 #include <unistd.h>
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7 #include "sickle.h"
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8 #include "kseq.h"
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9
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10
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11 void print_record (FILE *fp, kseq_t *fqr, cutsites *cs) {
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12 fprintf(fp, "@%s", fqr->name.s);
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13 if (fqr->comment.l) fprintf(fp, " %s\n", fqr->comment.s);
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14 else fprintf(fp, "\n");
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15 fprintf(fp, "%.*s\n", cs->three_prime_cut - cs->five_prime_cut, fqr->seq.s + cs->five_prime_cut);
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16 fprintf(fp, "+\n");
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17 fprintf(fp, "%.*s\n", cs->three_prime_cut - cs->five_prime_cut, fqr->qual.s + cs->five_prime_cut);
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18 }
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19
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20 void print_record_gzip (gzFile fp, kseq_t *fqr, cutsites *cs) {
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21 gzprintf(fp, "@%s", fqr->name.s);
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22 if (fqr->comment.l) gzprintf(fp, " %s\n", fqr->comment.s);
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23 else gzprintf(fp, "\n");
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24 gzprintf(fp, "%.*s\n", cs->three_prime_cut - cs->five_prime_cut, fqr->seq.s + cs->five_prime_cut);
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25 gzprintf(fp, "+\n");
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26 gzprintf(fp, "%.*s\n", cs->three_prime_cut - cs->five_prime_cut, fqr->qual.s + cs->five_prime_cut);
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27 }
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28
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29 void print_record_N (FILE *fp, kseq_t *fqr, int qualtype) {
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30 fprintf(fp, "@%s", fqr->name.s);
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31 if (fqr->comment.l) fprintf(fp, " %s\n", fqr->comment.s);
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32 else fprintf(fp, "\n");
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33 fprintf(fp, "N\n+\n%c\n", quality_constants[qualtype][Q_MIN]);
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34 }
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35
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36 void print_record_N_gzip (gzFile fp, kseq_t *fqr, int qualtype) {
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37 gzprintf(fp, "@%s", fqr->name.s);
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38 if (fqr->comment.l) gzprintf(fp, " %s\n", fqr->comment.s);
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39 else gzprintf(fp, "\n");
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40 gzprintf(fp, "N\n+\n%c\n", quality_constants[qualtype][Q_MIN]);
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41 }
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42
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