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1 #ifndef BWA_MAIN_H
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2 #define BWA_MAIN_H
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3
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4 #ifdef __cplusplus
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5 extern "C" {
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6 #endif
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7
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8 int bwa_fa2pac(int argc, char *argv[]);
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9 int bwa_pac_rev(int argc, char *argv[]);
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10 int bwa_pac2cspac(int argc, char *argv[]);
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11 int bwa_pac2bwt(int argc, char *argv[]);
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12 int bwa_bwtupdate(int argc, char *argv[]);
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13 int bwa_bwt2sa(int argc, char *argv[]);
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14 int bwa_index(int argc, char *argv[]);
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15 int bwa_aln(int argc, char *argv[]);
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16 int bwt_bwtgen_main(int argc, char *argv[]);
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17
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18 int bwa_sai2sam_se(int argc, char *argv[]);
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19 int bwa_sai2sam_pe(int argc, char *argv[]);
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20
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21 int bwa_stdsw(int argc, char *argv[]);
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22
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23 int bwa_bwtsw2(int argc, char *argv[]);
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24
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25 #ifdef __cplusplus
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26 }
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27 #endif
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28
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29 #endif
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