diff --git a/samtools-0.1.13/bam_maqcns.h b/samtools-0.1.13/bam_maqcns.h new file mode 100644 --- /dev/null +++ b/samtools-0.1.13/bam_maqcns.h @@ -0,0 +1,61 @@ +#ifndef BAM_MAQCNS_H +#define BAM_MAQCNS_H + +#include "glf.h" + +#define BAM_ERRMOD_MAQ2 0 +#define BAM_ERRMOD_MAQ 1 +#define BAM_ERRMOD_SOAP 2 + +struct __bmc_aux_t; + +typedef struct { + float het_rate, theta; + int n_hap, cap_mapQ, errmod, min_baseQ; + + float eta, q_r; + double *fk, *coef; + double *lhet; + struct __bmc_aux_t *aux; +} bam_maqcns_t; + +typedef struct { + int q_indel; // indel sequencing error, phred scaled + float r_indel; // indel prior + float r_snp; // snp prior + // hidden parameters, unchangeable from command line + int mm_penalty, indel_err, ambi_thres; +} bam_maqindel_opt_t; + +typedef struct { + int indel1, indel2; + int cnt1, cnt2, cnt_anti; + int cnt_ref, cnt_ambi; + char *s[2]; + // + int gt, gl[2]; + int q_cns, q_ref; +} bam_maqindel_ret_t; + +#ifdef __cplusplus +extern "C" { +#endif + + bam_maqcns_t *bam_maqcns_init(); + void bam_maqcns_prepare(bam_maqcns_t *bm); + void bam_maqcns_destroy(bam_maqcns_t *bm); + glf1_t *bam_maqcns_glfgen(int n, const bam_pileup1_t *pl, uint8_t ref_base, bam_maqcns_t *bm); + uint32_t bam_maqcns_call(int n, const bam_pileup1_t *pl, bam_maqcns_t *bm); + // return: cns<<28 | cns2<<24 | mapQ<<16 | cnsQ<<8 | cnsQ2 + uint32_t glf2cns(const glf1_t *g, int q_r); + + bam_maqindel_opt_t *bam_maqindel_opt_init(); + bam_maqindel_ret_t *bam_maqindel(int n, int pos, const bam_maqindel_opt_t *mi, const bam_pileup1_t *pl, const char *ref, + int _n_types, int *_types); + void bam_maqindel_ret_destroy(bam_maqindel_ret_t*); + +#ifdef __cplusplus +} +#endif + +#endif diff --git a/samtools-0.1.13/bgzf.h b/samtools-0.1.13/bgzf.h new file mode 100644 --- /dev/null +++ b/samtools-0.1.13/bgzf.h @@ -0,0 +1,157 @@ +/* The MIT License + + Copyright (c) 2008 Broad Institute / Massachusetts Institute of Technology + + Permission is hereby granted, free of charge, to any person obtaining a copy + of this software and associated documentation files (the "Software"), to deal + in the Software without restriction, including without limitation the rights + to use, copy, modify, merge, publish, distribute, sublicense, and/or sell + copies of the Software, and to permit persons to whom the Software is + furnished to do so, subject to the following conditions: + + The above copyright notice and this permission notice shall be included in + all copies or substantial portions of the Software. + + THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR + IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, + FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE + AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER + LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, + OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN + THE SOFTWARE. +*/ + +#ifndef __BGZF_H +#define __BGZF_H + +#include +#include +#include +#include +#ifdef _USE_KNETFILE +#include "knetfile.h" +#endif + +//typedef int8_t bool; + +typedef struct { + int file_descriptor; + char open_mode; // 'r' or 'w' + bool owned_file, is_uncompressed; +#ifdef _USE_KNETFILE + union { + knetFile *fpr; + FILE *fpw; + } x; +#else + FILE* file; +#endif + int uncompressed_block_size; + int compressed_block_size; + void* uncompressed_block; + void* compressed_block; + int64_t block_address; + int block_length; + int block_offset; + int cache_size; + const char* error; + void *cache; // a pointer to a hash table +} BGZF; + +#ifdef __cplusplus +extern "C" { +#endif + +/* + * Open an existing file descriptor for reading or writing. + * Mode must be either "r" or "w". + * A subsequent bgzf_close will not close the file descriptor. + * Returns null on error. + */ +BGZF* bgzf_fdopen(int fd, const char* __restrict mode); + +/* + * Open the specified file for reading or writing. + * Mode must be either "r" or "w". + * Returns null on error. + */ +BGZF* bgzf_open(const char* path, const char* __restrict mode); + +/* + * Close the BGZ file and free all associated resources. + * Does not close the underlying file descriptor if created with bgzf_fdopen. + * Returns zero on success, -1 on error. + */ +int bgzf_close(BGZF* fp); + +/* + * Read up to length bytes from the file storing into data. + * Returns the number of bytes actually read. + * Returns zero on end of file. + * Returns -1 on error. + */ +int bgzf_read(BGZF* fp, void* data, int length); + +/* + * Write length bytes from data to the file. + * Returns the number of bytes written. + * Returns -1 on error. + */ +int bgzf_write(BGZF* fp, const void* data, int length); + +/* + * Return a virtual file pointer to the current location in the file. + * No interpetation of the value should be made, other than a subsequent + * call to bgzf_seek can be used to position the file at the same point. + * Return value is non-negative on success. + * Returns -1 on error. + */ +#define bgzf_tell(fp) ((fp->block_address << 16) | (fp->block_offset & 0xFFFF)) + +/* + * Set the file to read from the location specified by pos, which must + * be a value previously returned by bgzf_tell for this file (but not + * necessarily one returned by this file handle). + * The where argument must be SEEK_SET. + * Seeking on a file opened for write is not supported. + * Returns zero on success, -1 on error. + */ +int64_t bgzf_seek(BGZF* fp, int64_t pos, int where); + +/* + * Set the cache size. Zero to disable. By default, caching is + * disabled. The recommended cache size for frequent random access is + * about 8M bytes. + */ +void bgzf_set_cache_size(BGZF *fp, int cache_size); + +int bgzf_check_EOF(BGZF *fp); +int bgzf_read_block(BGZF* fp); +int bgzf_flush(BGZF* fp); +int bgzf_flush_try(BGZF *fp, int size); + +#ifdef __cplusplus +} +#endif + +static inline int bgzf_getc(BGZF *fp) +{ + int c; + if (fp->block_offset >= fp->block_length) { + if (bgzf_read_block(fp) != 0) return -2; /* error */ + if (fp->block_length == 0) return -1; /* end-of-file */ + } + c = ((unsigned char*)fp->uncompressed_block)[fp->block_offset++]; + if (fp->block_offset == fp->block_length) { +#ifdef _USE_KNETFILE + fp->block_address = knet_tell(fp->x.fpr); +#else + fp->block_address = ftello(fp->file); +#endif + fp->block_offset = 0; + fp->block_length = 0; + } + return c; +} + +#endif diff --git a/samtools-0.1.13/errmod.h b/samtools-0.1.13/errmod.h new file mode 100644 --- /dev/null +++ b/samtools-0.1.13/errmod.h @@ -0,0 +1,24 @@ +#ifndef ERRMOD_H +#define ERRMOD_H + +#include + +struct __errmod_coef_t; + +typedef struct { + double depcorr; + struct __errmod_coef_t *coef; +} errmod_t; + +errmod_t *errmod_init(float depcorr); +void errmod_destroy(errmod_t *em); + +/* + n: number of bases + m: maximum base + bases[i]: qual:6, strand:1, base:4 + q[i*m+j]: phred-scaled likelihood of (i,j) + */ +int errmod_cal(const errmod_t *em, int n, int m, uint16_t *bases, float *q); + +#endif diff --git a/samtools-0.1.13/kaln.h b/samtools-0.1.13/kaln.h new file mode 100644 --- /dev/null +++ b/samtools-0.1.13/kaln.h @@ -0,0 +1,67 @@ +/* The MIT License + + Copyright (c) 2003-2006, 2008, 2009 by Heng Li + + Permission is hereby granted, free of charge, to any person obtaining + a copy of this software and associated documentation files (the + "Software"), to deal in the Software without restriction, including + without limitation the rights to use, copy, modify, merge, publish, + distribute, sublicense, and/or sell copies of the Software, and to + permit persons to whom the Software is furnished to do so, subject to + the following conditions: + + The above copyright notice and this permission notice shall be + included in all copies or substantial portions of the Software. + + THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, + EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF + MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND + NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS + BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN + ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN + CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE + SOFTWARE. +*/ + +#ifndef LH3_KALN_H_ +#define LH3_KALN_H_ + +#include + +#define MINOR_INF -1073741823 + +typedef struct { + int gap_open; + int gap_ext; + int gap_end_open; + int gap_end_ext; + + int *matrix; + int row; + int band_width; +} ka_param_t; + +typedef struct { + int iio, iie, ido, ide; + int eio, eie, edo, ede; + int *matrix; + int row; + int band_width; +} ka_param2_t; + +#ifdef __cplusplus +extern "C" { +#endif + + uint32_t *ka_global_core(uint8_t *seq1, int len1, uint8_t *seq2, int len2, const ka_param_t *ap, + int *_score, int *n_cigar); + int ka_global_score(const uint8_t *_seq1, int len1, const uint8_t *_seq2, int len2, const ka_param2_t *ap); +#ifdef __cplusplus +} +#endif + +extern ka_param_t ka_param_blast; /* = { 5, 2, 5, 2, aln_sm_blast, 5, 50 }; */ +extern ka_param_t ka_param_qual; // only use this for global alignment!!! +extern ka_param2_t ka_param2_qual; // only use this for global alignment!!! + +#endif diff --git a/samtools-0.1.13/knetfile.h b/samtools-0.1.13/knetfile.h new file mode 100644 --- /dev/null +++ b/samtools-0.1.13/knetfile.h @@ -0,0 +1,75 @@ +#ifndef KNETFILE_H +#define KNETFILE_H + +#include +#include + +#ifndef _WIN32 +#define netread(fd, ptr, len) read(fd, ptr, len) +#define netwrite(fd, ptr, len) write(fd, ptr, len) +#define netclose(fd) close(fd) +#else +#include +#define netread(fd, ptr, len) recv(fd, ptr, len, 0) +#define netwrite(fd, ptr, len) send(fd, ptr, len, 0) +#define netclose(fd) closesocket(fd) +#endif + +// FIXME: currently I/O is unbuffered + +#define KNF_TYPE_LOCAL 1 +#define KNF_TYPE_FTP 2 +#define KNF_TYPE_HTTP 3 + +typedef struct knetFile_s { + int type, fd; + int64_t offset; + char *host, *port; + + // the following are for FTP only + int ctrl_fd, pasv_ip[4], pasv_port, max_response, no_reconnect, is_ready; + char *response, *retr, *size_cmd; + int64_t seek_offset; // for lazy seek + int64_t file_size; + + // the following are for HTTP only + char *path, *http_host; +} knetFile; + +#define knet_tell(fp) ((fp)->offset) +#define knet_fileno(fp) ((fp)->fd) + +#ifdef __cplusplus +extern "C" { +#endif + +#ifdef _WIN32 + int knet_win32_init(); + void knet_win32_destroy(); +#endif + + knetFile *knet_open(const char *fn, const char *mode); + + /* + This only works with local files. + */ + knetFile *knet_dopen(int fd, const char *mode); + + /* + If ->is_ready==0, this routine updates ->fd; otherwise, it simply + reads from ->fd. + */ + off_t knet_read(knetFile *fp, void *buf, off_t len); + + /* + This routine only sets ->offset and ->is_ready=0. It does not + communicate with the FTP server. + */ + off_t knet_seek(knetFile *fp, int64_t off, int whence); + int knet_close(knetFile *fp); + +#ifdef __cplusplus +} +#endif + +#endif diff --git a/samtools-0.1.13/kprobaln.h b/samtools-0.1.13/kprobaln.h new file mode 100644 --- /dev/null +++ b/samtools-0.1.13/kprobaln.h @@ -0,0 +1,49 @@ +/* The MIT License + + Copyright (c) 2003-2006, 2008, 2009 by Heng Li + + Permission is hereby granted, free of charge, to any person obtaining + a copy of this software and associated documentation files (the + "Software"), to deal in the Software without restriction, including + without limitation the rights to use, copy, modify, merge, publish, + distribute, sublicense, and/or sell copies of the Software, and to + permit persons to whom the Software is furnished to do so, subject to + the following conditions: + + The above copyright notice and this permission notice shall be + included in all copies or substantial portions of the Software. + + THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, + EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF + MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND + NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS + BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN + ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN + CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE + SOFTWARE. +*/ + +#ifndef LH3_KPROBALN_H_ +#define LH3_KPROBALN_H_ + +#include + +typedef struct { + float d, e; + int bw; +} kpa_par_t; + +#ifdef __cplusplus +extern "C" { +#endif + + int kpa_glocal(const uint8_t *_ref, int l_ref, const uint8_t *_query, int l_query, const uint8_t *iqual, + const kpa_par_t *c, int *state, uint8_t *q); + +#ifdef __cplusplus +} +#endif + +extern kpa_par_t kpa_par_def, kpa_par_alt; + +#endif diff --git a/samtools.cabal b/samtools.cabal --- a/samtools.cabal +++ b/samtools.cabal @@ -1,5 +1,5 @@ Name: samtools -Version: 0.1 +Version: 0.1.1 Synopsis: Binding to the C samtools library Description: Binding to the C samtools library, which reads and writes SAM format alignments, both binary and tab- @@ -49,8 +49,10 @@ samtools-0.1.13/bam.h, samtools-0.1.13/bam_endian.h, samtools-0.1.13/faidx.h, samtools-0.1.13/glf.h, samtools-0.1.13/khash.h, samtools-0.1.13/kseq.h, samtools-0.1.13/ksort.h, samtools-0.1.13/kstring.h, - samtools-0.1.13/razf.h, samtools-0.1.13/sam.h, samtools-0.1.13/sam_header.h - CC-options: -g -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -Wno-unused-result + samtools-0.1.13/razf.h, samtools-0.1.13/sam.h, samtools-0.1.13/sam_header.h, + samtools-0.1.13/bgzf.h, samtools-0.1.13/knetfile.h, samtools-0.1.13/kaln.h, + samtools-0.1.13/kprobaln.h, samtools-0.1.13/bam_maqcns.h, samtools-0.1.13/errmod.h + CC-options: -g -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE Extra-libraries: z Ghc-options: -Wall @@ -77,7 +79,9 @@ samtools-0.1.13/bam.h, samtools-0.1.13/bam_endian.h, samtools-0.1.13/faidx.h, samtools-0.1.13/glf.h, samtools-0.1.13/khash.h, samtools-0.1.13/kseq.h, samtools-0.1.13/ksort.h, samtools-0.1.13/kstring.h, - samtools-0.1.13/razf.h, samtools-0.1.13/sam.h, samtools-0.1.13/sam_header.h - CC-options: -g -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -Wno-unused-result + samtools-0.1.13/razf.h, samtools-0.1.13/sam.h, samtools-0.1.13/sam_header.h, + samtools-0.1.13/bgzf.h, samtools-0.1.13/knetfile.h, samtools-0.1.13/kaln.h, + samtools-0.1.13/kprobaln.h, samtools-0.1.13/bam_maqcns.h, samtools-0.1.13/errmod.h + CC-options: -g -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE Extra-libraries: z Ghc-options: -Wall diff --git a/src/Bio/SamTools/LowLevel.chs b/src/Bio/SamTools/LowLevel.chs --- a/src/Bio/SamTools/LowLevel.chs +++ b/src/Bio/SamTools/LowLevel.chs @@ -46,6 +46,8 @@ import Control.Monad import qualified Data.ByteString.Char8 as BS +#undef __BLOCKS__ + #include "faidx.h" #include "sam.h" #include "samtools.h"