Commit 5441f495 authored by Andreas Tille's avatar Andreas Tille
Browse files

New upstream version 2.1.4

parent 7871ef7d

.travis.yml

+6 −6
Original line number Diff line number Diff line
@@ -33,10 +33,10 @@ sudo: false 
# Copied from https://github.com/nim-lang/Nim/wiki/TravisCI

#language: c

env:

  # Build and test against the master and devel branches of Nim

  #- BRANCH=master

  - BRANCH=devel

  #- BRANCH=v0.17.2

  # Build and test against the master and/or devel branches of Nim

  - BRANCH=master

  #- BRANCH=devel

  #- BRANCH=v0.18.0

compiler:

  # Build and test using both gcc and clang

  - gcc
@@ -76,8 +76,8 @@ before_script: 
#    - nim doc --docSeeSrcUrl:https://github.com/AUTHOR/MYPROJECT/blob/master --project MYFILE.nim

cache:

  directories:

    #- nim-master

    - nim-devel

    - nim-master

    #- nim-devel

branches:

  except:

    - gh-pages

DALIGNER/DB.c

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DALIGNER/DB.h

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DALIGNER/DB2Falcon.c

+3 −3
Original line number Diff line number Diff line
@@ -16,7 +16,7 @@ 
static char *Usage = "[-U] [-w<int(80)>] <path:db>";



int main(int argc, char *argv[])

{ HITS_DB    _db, *db = &_db;

{ DAZZ_DB    _db, *db = &_db;

  FILE       *dbfile;

  int         nfiles;

  int         UPPER, WIDTH;
@@ -83,7 +83,7 @@ int main(int argc, char *argv[]) 


  //  For each file do:



  { HITS_READ  *reads;

  { DAZZ_READ  *reads;

    char       *read;

    int         f, first;

    FILE *ofile;
@@ -107,7 +107,7 @@ int main(int argc, char *argv[]) 


        for (i = first; i < last && i <  db->nreads; i++)

          { int        j, len;

            HITS_READ *r;

            DAZZ_READ *r;



            r     = reads + i;

            len   = r->rlen;

DALIGNER/DBX.c

+6 −6
Original line number Diff line number Diff line
@@ -6,7 +6,7 @@ 
#include <assert.h>



// From Jason, with 1 change

static char* Load_Read_Data(HITS_DB *db) {

static char* Load_Read_Data(DAZZ_DB *db) {

  FILE  *bases  = (FILE*) db->bases;

  struct stat sbuf;

  char  *data;
@@ -22,7 +22,7 @@ static char* Load_Read_Data(HITS_DB *db) { 
}



// Wrapper

int Open_DBX(char *path, HITS_DBX *dbx, bool preload) {

int Open_DBX(char *path, DAZZ_DBX *dbx, bool preload) {

  dbx->data = NULL;

  int rc = Open_DB(path, &dbx->db);

  switch (rc) {
@@ -44,10 +44,10 @@ int Open_DBX(char *path, HITS_DBX *dbx, bool preload) { 
}



// From Jason

static int Load_Read_From_RAM(HITS_DB *db, char *data, int i, char *read, int ascii) {

static int Load_Read_From_RAM(DAZZ_DB *db, char *data, int i, char *read, int ascii) {

  int64      off;

  int        len, clen;

  HITS_READ *r = db->reads;

  DAZZ_READ *r = db->reads;



  if (i >= db->nreads) { EXIT(1); }
@@ -70,7 +70,7 @@ static int Load_Read_From_RAM(HITS_DB *db, char *data, int i, char *read, int as 
}



// Wrapper

int Load_ReadX(HITS_DBX *dbx, int i, char *read, int ascii) {

int Load_ReadX(DAZZ_DBX *dbx, int i, char *read, int ascii) {

  if (dbx->data) {

    return Load_Read_From_RAM(&dbx->db, dbx->data, i, read, ascii);

  } else {
@@ -79,7 +79,7 @@ int Load_ReadX(HITS_DBX *dbx, int i, char *read, int ascii) { 
}



// Wrapper

void Close_DBX(HITS_DBX *dbx) {

void Close_DBX(DAZZ_DBX *dbx) {

  Close_DB(&dbx->db);

  if (dbx->data) free(dbx->data);

}