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jpayne@68
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1 # cython: language_level=3
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2 from pysam.libcalignmentfile cimport AlignedSegment, AlignmentFile
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3
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4 #################################################
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5 # Compatibility Layer for pysam < 0.8
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6
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7 # import all declarations from htslib
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8 from pysam.libchtslib cimport *
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9
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10 cdef class AlignedRead(AlignedSegment):
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11 pass
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12
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13 cdef class Samfile(AlignmentFile):
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14 pass
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15
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16 # import the conversion functions
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17 cdef extern from "htslib_util.h":
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18
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19 # add *nbytes* into the variable length data of *src* at *pos*
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20 bam1_t * pysam_bam_update(bam1_t * b,
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21 size_t nbytes_old,
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22 size_t nbytes_new,
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23 uint8_t * pos)
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24
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25 # now: static
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26 int aux_type2size(int)
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27
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28 char * pysam_bam_get_qname(bam1_t * b)
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29 uint32_t * pysam_bam_get_cigar(bam1_t * b)
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30 uint8_t * pysam_bam_get_seq(bam1_t * b)
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31 uint8_t * pysam_bam_get_qual(bam1_t * b)
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32 uint8_t * pysam_bam_get_aux(bam1_t * b)
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33 int pysam_bam_get_l_aux(bam1_t * b)
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34 char pysam_bam_seqi(uint8_t * s, int i)
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35
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36 uint16_t pysam_get_bin(bam1_t * b)
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37 uint8_t pysam_get_qual(bam1_t * b)
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38 uint8_t pysam_get_l_qname(bam1_t * b)
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39 uint16_t pysam_get_flag(bam1_t * b)
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40 uint32_t pysam_get_n_cigar(bam1_t * b)
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41 void pysam_set_bin(bam1_t * b, uint16_t v)
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42 void pysam_set_qual(bam1_t * b, uint8_t v)
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43 void pysam_set_l_qname(bam1_t * b, uint8_t v)
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44 void pysam_set_flag(bam1_t * b, uint16_t v)
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45 void pysam_set_n_cigar(bam1_t * b, uint32_t v)
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46 void pysam_update_flag(bam1_t * b, uint16_t v, uint16_t flag)
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