HTS.c

#include "htslib/sam.h"

int inline_c_Bio_HTS_0_0efc6161c1b66bc79e862910b9e93f1d32ddc02d(htsFile * fp_inline_c_0, bam1_t * b_inline_c_1) {
return ( bam_write1(fp_inline_c_0->fp.bgzf, b_inline_c_1) );
}


int inline_c_Bio_HTS_1_0c54bc94ad2e32d428064e2a5c26a7036890b9a6(htsFile * fp_inline_c_0, bam_hdr_t * hdr_inline_c_1) {
return (
                        bam_hdr_write(fp_inline_c_0->fp.bgzf, hdr_inline_c_1) );
}


htsFile * inline_c_Bio_HTS_2_07f3fede9c57363b6e41738becd5a00d64df9d5c(char * fn_27_inline_c_0) {
return ( hts_open(fn_27_inline_c_0, "r") );
}


htsFile * inline_c_Bio_HTS_3_4af84655e4829571c79edc68791d221a719c60ab(char * fn_27_inline_c_0) {
return ( hts_open(fn_27_inline_c_0, "wb") );
}


void inline_c_Bio_HTS_4_d667db7c61cb0de3c96f1d806701fe63606a1af0(htsFile * h_inline_c_0) {
 hts_close(h_inline_c_0) ;
}


bam_hdr_t * inline_c_Bio_HTS_5_9a30278929e5b8570bc58dc24e83fd868ec2513f(htsFile * h_inline_c_0) {
return ( bam_hdr_read(h_inline_c_0->fp.bgzf) );
}


char * inline_c_Bio_HTS_6_5a31ba58a253c55850867b8802710825075bca03(bam_hdr_t * hdr_inline_c_0) {
return ( hdr_inline_c_0->text );
}


bam1_t * inline_c_Bio_HTS_7_25f5b2f49b2eac08644b77f5a1c27030b81e5dc3(int * r_inline_c_0, htsFile * h_inline_c_1) {

            bam1_t *b = bam_init1();
            *r_inline_c_0 = bam_read1(h_inline_c_1->fp.bgzf, b);
            return b;
        
}


int32_t inline_c_Bio_HTS_8_8e12d9d09c24fcc6b41593e5bc03c97f756f6da1(bam1_t * b_inline_c_0) {
return ( b_inline_c_0->core.tid );
}


char * inline_c_Bio_HTS_9_31676430ec791ba4f73764dc21c992d6d39307fc(bam_hdr_t * h_inline_c_0, int32_t i_inline_c_1) {
return ( h_inline_c_0->target_name[i_inline_c_1] );
}


int32_t inline_c_Bio_HTS_10_c89b42fc83db79c1cd226594b3a86cd92b81f38b(bam1_t * b_inline_c_0) {
return ( b_inline_c_0->core.pos );
}


int32_t inline_c_Bio_HTS_11_cc329ca55a7e13133af0b3dbb6abb3edc854b65e(bam1_t * b_inline_c_0) {
return ( bam_endpos(b_inline_c_0) );
}


int32_t inline_c_Bio_HTS_12_6fb2dbf3d90d4141663e524757f874dcf05a03e4(bam1_t * b_inline_c_0) {
return ( b_inline_c_0->core.l_qseq );
}


int inline_c_Bio_HTS_13_44d7a287b2cc95c82e760427675196e1ba7261a1(bam1_t * b_inline_c_0) {
return (bam_is_rev(b_inline_c_0) );
}


uint16_t inline_c_Bio_HTS_14_12453aaa173031b617539dcd57698955b11bd327(bam1_t * b_inline_c_0) {
return ( b_inline_c_0->core.flag );
}


uint8_t inline_c_Bio_HTS_15_49728fef988bc0954110504a26677faa43ce6ce9(bam1_t * b_inline_c_0) {
return ( b_inline_c_0->core.qual );
}


int32_t inline_c_Bio_HTS_16_6fb2dbf3d90d4141663e524757f874dcf05a03e4(bam1_t * b_inline_c_0) {
return ( b_inline_c_0->core.l_qseq );
}


void inline_c_Bio_HTS_17_ed1829c64b8823aa1711ba319219f175ed965ce4(bam1_t * b_inline_c_0, int32_t l_inline_c_1, char * str_inline_c_2) {

                        int32_t i;
                        uint8_t *s = bam_get_seq(b_inline_c_0);
                        for (i = 0; i < l_inline_c_1; ++i)
                            str_inline_c_2[i] = "=ACMGRSVTWYHKDBN"[bam_seqi(s, i)];
                    
}


char * inline_c_Bio_HTS_18_7083ac4175bb445932400343a035586aa327afa8(bam1_t * b_inline_c_0) {
return (bam_get_qname(b_inline_c_0) );
}


int32_t inline_c_Bio_HTS_19_6fb2dbf3d90d4141663e524757f874dcf05a03e4(bam1_t * b_inline_c_0) {
return ( b_inline_c_0->core.l_qseq );
}


int8_t inline_c_Bio_HTS_20_ff7eee4e1210259019f9cd0f9e269fdcf8ed1666(bam1_t * b_inline_c_0) {

                        uint8_t *s = bam_get_qual(b_inline_c_0);
                        return (s[0] == 0xff);
                     
}


void inline_c_Bio_HTS_21_4b537c6c8c081040b4dd320c93ee949f58ac34df(bam1_t * b_inline_c_0, int32_t l_inline_c_1, char * str_inline_c_2) {

                                int32_t i;
                                uint8_t *s = bam_get_qual(b_inline_c_0);
                                for (i = 0; i < l_inline_c_1; ++i)
                                    str_inline_c_2[i] = s[i];
                            
}


uint16_t inline_c_Bio_HTS_22_ba4509ac6cfa51e21b3315e1bc0c79664332c151(bam1_t * b_inline_c_0) {
return ( b_inline_c_0->core.n_cigar );
}


void inline_c_Bio_HTS_23_04238a6d67efdaba04e6fe62c62067daa422dedb(bam1_t * b_inline_c_0, uint16_t n_inline_c_1, int * num_inline_c_2, char * str_inline_c_3) {

                            uint16_t i;
                            uint32_t *cigar = bam_get_cigar(b_inline_c_0);
                            for (i = 0; i < n_inline_c_1; ++i) {
                                num_inline_c_2[i] = bam_cigar_oplen(cigar[i]);
                                str_inline_c_3[i] = bam_cigar_opchr(cigar[i]);
                            }
                         
}


int32_t inline_c_Bio_HTS_24_a6dc5594b24fbf473396136e59bcee0228785fc4(bam1_t * b_inline_c_0) {
return ( b_inline_c_0->core.mtid );
}


char * inline_c_Bio_HTS_25_31676430ec791ba4f73764dc21c992d6d39307fc(bam_hdr_t * h_inline_c_0, int32_t i_inline_c_1) {
return ( h_inline_c_0->target_name[i_inline_c_1] );
}


int32_t inline_c_Bio_HTS_26_54a6e402cf38aa9b617612b54be97e879e2b17b7(bam1_t * b_inline_c_0) {
return ( b_inline_c_0->core.mpos );
}


int32_t inline_c_Bio_HTS_27_14020e59f59859519591c231f45ae2ab8f85c395(bam1_t * b_inline_c_0) {
return ( b_inline_c_0->core.isize );
}