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Viewing changes to src/samprint.h

Committer: Package Import Robot
Author(s): Shaun Jackman
Date: 2011-12-07 10:46:12 UTC
mfrom: (1.1.9)
Revision ID: package-import@ubuntu.com-20111207104612-4jdx1gj67oi1tx0w

Tags: 2011-11-30-1

New upstream release.

files modified:
ChangeLog

VERSION

configure

configure.ac

debian/changelog

debian/gmap.1

debian/gmap_setup.1

debian/gsnap.1

src/atoiindex.c

src/cmetindex.c

src/diag.c

src/dynprog.c

src/dynprog.h

src/gmap.c

src/gmapindex.c

src/goby.c

src/gsnap.c

src/list.c

src/list.h

src/maxent_hr.c

src/maxent_hr.h

src/outbuffer.c

src/outbuffer.h

src/pair.c

src/pair.h

src/pairpool.c

src/pairpool.h

src/result.c

src/result.h

src/resulthr.c

src/resulthr.h

src/samprint.c

src/samprint.h

src/shortread.c

src/shortread.h

src/smooth.c

src/splicetrie.c

src/splicetrie.h

src/splicetrie_build.c

src/stage1.c

src/stage1hr.c

src/stage1hr.h

src/stage2.c

src/stage2.h

src/stage3.c

src/stage3.h

src/stage3hr.c

src/stage3hr.h

src/substring.c

src/substring.h

util/gmap_build.pl.in

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src/samprint.h

/* $Id: samprint.h 40271 2011-05-28 02:29:18Z twu $ */

/* $Id: samprint.h 53168 2011-11-28 02:55:16Z twu $ */

#ifndef SAMPRINT_INCLUDED

#define SAMPRINT_INCLUDED

#include "substring.h"

#include "bool.h"

extern void

SAM_setup (bool quiet_if_excessive_p_in, int maxpaths_in);

extern Genomicpos_T

SAM_compute_chrpos (int *hardclip_low, int *hardclip_high, Stage3end_T this,

Substring_T substring_low, int querylength);

extern void

SAM_print (FILE *fp, Stage3end_T this, Stage3end_T mate, char *acc, int pathnum, int npaths,

int score, IIT_T chromosome_iit, Shortread_T queryseq,

int absmq_score, int second_absmq, int mapq_score, IIT_T chromosome_iit, Shortread_T queryseq,

Shortread_T queryseq2, int pairedlength, Genomicpos_T chrpos, Genomicpos_T mate_chrpos,

int hardclip_low, int hardclip_high, Resulttype_T resulttype, bool first_read_p,

int npaths_mate, int quality_shift, char *sam_read_group_id, bool invertp, bool invert_mate_p);

int npaths_mate, int quality_shift, char *sam_read_group_id, bool invertp, bool invert_mate_p,

bool merge_samechr_p);

extern void

SAM_print_paired (Result_T result, Resulttype_T resulttype,

IIT_T chromosome_iit, Shortread_T queryseq1, Shortread_T queryseq2,

int maxpaths, bool quiet_if_excessive_p,

bool invert_first_p, bool invert_second_p,

bool nofailsp, bool failsonlyp, bool fails_as_input_p,

bool fastq_format_p, bool clip_overlap_p, int quality_shift, char *sam_read_group_id,

bool fastq_format_p, bool clip_overlap_p, bool merge_samechr_p,

int quality_shift, char *sam_read_group_id,

FILE *fp_nomapping_1, FILE *fp_nomapping_2,

FILE *fp_unpaired_uniq, FILE *fp_unpaired_transloc, FILE *fp_unpaired_mult,

FILE *fp_halfmapping_uniq, FILE *fp_halfmapping_transloc, FILE *fp_halfmapping_mult,

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