fix spelling typos

dont_link_pthread

override_version

hardening-flags

spelling

From: Michael R. Crusoe <michael.crusoe@gmail.com>

Subject: lintian-inspired spelling fixes

--- libvcflib.orig/src/abba-baba.cpp

+++ libvcflib/src/abba-baba.cpp

@@ -47,7 +47,7 @@

   cerr << "INFO: usage:  abba-baba --tree 0,1,2,3 --file my.vcf --type PL" << endl;

   cerr << endl;

-  cerr << "INFO: required: t,tree       -- a zero based comma seperated list of target individuals corrisponding to VCF columns" << endl;

+  cerr << "INFO: required: t,tree       -- a zero based comma separated list of target individuals corrisponding to VCF columns" << endl;

   cerr << "INFO: required: f,file       -- a properly formatted VCF.                                                           " << endl;

   cerr << "INFO: required: y,type       -- genotype likelihood format ; genotypes: GP,GL or PL;                                " << endl;

   cerr << endl;

--- libvcflib.orig/src/gl-XPEHH.cpp

+++ libvcflib/src/gl-XPEHH.cpp

@@ -488,8 +488,8 @@

 	    cerr << "INFO: gl-XPEHH  --target 0,1,2,3,4,5,6,7 --background 11,12,13,16,17,19,22 --file my.vcf --deltaaf 0.1 --ancestral 0        " << endl;

 	    cerr << endl;

 	    cerr << "INFO: required: r,region     -- a genomice range to calculate gl-XPEHH on in the format : \"seqid:start-end]\" or \"seqid\" " << endl;

-	    cerr << "INFO: required: t,target     -- a zero base comma seperated list of target individuals corrisponding to VCF columns        " << endl;

-	    cerr << "INFO: required: b,background -- a zero base comma seperated list of background individuals corrisponding to VCF columns    " << endl;

+	    cerr << "INFO: required: t,target     -- a zero base comma separated list of target individuals corrisponding to VCF columns        " << endl;

+	    cerr << "INFO: required: b,background -- a zero base comma separated list of background individuals corrisponding to VCF columns    " << endl;

 	    cerr << "INFO: required: f,file a     -- proper formatted VCF.  the FORMAT field MUST contain \"PL\" if option phased == 0           " << endl; 

 	    cerr << "INFO: optional: m,mutation   -- which state is derived in vcf [0,1] default is 1                                            " << endl;

 	    cerr << "INFO: optional: p,phased     -- phasing flag [0,1] 0 = phase vcf, 1 = vcf is already phased                                 " << endl;

--- libvcflib.orig/src/hapLrt.cpp

+++ libvcflib/src/hapLrt.cpp

@@ -24,7 +24,7 @@

   cerr << endl << endl;

   cerr << "INFO: help" << endl;

   cerr << "INFO: description:" << endl;

-  cerr << "     HapLRT is a likelihood ratio test for haplotype lengths.  The lengths are modeled with an exponential distribtuion.  " << endl;

+  cerr << "     HapLRT is a likelihood ratio test for haplotype lengths.  The lengths are modeled with an exponential distribution.  " << endl;

   cerr << "     The sign denotes if the target has longer haplotypes (1) or the background (-1).                                     " << endl << endl;

   cerr << "Output : 4 columns :                             " << endl;

@@ -38,8 +38,8 @@

   cerr << "INFO: hapLRT  --target 0,1,2,3,4,5,6,7 --background 11,12,13,16,17,19,22 --type GP --file my.vcf                                     " << endl;

   cerr << endl;

-  cerr << "INFO: required: t,target     -- argument: a zero base comma seperated list of target individuals corrisponding to VCF columns        " << endl;

-  cerr << "INFO: required: b,background -- argument: a zero base comma seperated list of background individuals corrisponding to VCF columns    " << endl;

+  cerr << "INFO: required: t,target     -- argument: a zero base comma separated list of target individuals corrisponding to VCF columns        " << endl;

+  cerr << "INFO: required: b,background -- argument: a zero base comma separated list of background individuals corrisponding to VCF columns    " << endl;

   cerr << "INFO: required: f,file       -- argument: a properly formatted phased VCF file                                                       " << endl;

   cerr << "INFO: required: y,type       -- argument: type of genotype likelihood: PL, GL or GP                                                  " << endl;

   cerr << "INFO: optional: r,region     -- argument: a genomice range to calculate hapLrt on in the format : \"seqid:start-end\" or \"seqid\" " << endl;

--- libvcflib.orig/src/vcfld.cpp

+++ libvcflib/src/vcfld.cpp

@@ -26,8 +26,8 @@

   cerr << "INFO: LD --target 0,1,2,3,4,5,6,7 --background 11,12,13,16,17,19,22 --file my.vcf -e -d -r                                           " << endl;

   cerr << endl;

-  cerr << "INFO: required: t,target     -- argument: a zero base comma seperated list of target individuals corrisponding to VCF columns        " << endl;

-  cerr << "INFO: required: b,background -- argument: a zero base comma seperated list of background individuals corrisponding to VCF columns    " << endl;

+  cerr << "INFO: required: t,target     -- argument: a zero base comma separated list of target individuals corrisponding to VCF columns        " << endl;

+  cerr << "INFO: required: b,background -- argument: a zero base comma separated list of background individuals corrisponding to VCF columns    " << endl;

   cerr << "INFO: required: f,file       -- argument: a properly formatted phased VCF file                                                       " << endl;

   cerr << "INFO: required: y,type       -- argument: type of genotype likelihood: PL, GL or GP                                                  " << endl;

   cerr << "INFO: optional: w,window     -- argument: window size to average LD; default is 1000                                                 " << endl;

--- libvcflib.orig/src/genotypeSummary.cpp

+++ libvcflib/src/genotypeSummary.cpp

@@ -356,7 +356,7 @@

             }

 	  }

 	  else{

-	    std::cerr << "FATAL: unkown genotype index" << std::endl;

+	    std::cerr << "FATAL: unknown genotype index" << std::endl;

 cerr << populationTarget->genoIndex[i] << endl;

 cerr << var << endl;

 	    exit(1);

--- libvcflib.orig/src/permuteGPAT++.cpp

+++ libvcflib/src/permuteGPAT++.cpp

@@ -169,7 +169,7 @@

    }

  }

  else{

-   cerr << "FATAL: coult not open file: " << globalOpts.file << endl;

+   cerr << "FATAL: could not open file: " << globalOpts.file << endl;

    exit(1);

  }

@@ -214,7 +214,7 @@

  }

  else{

-   cerr << "FATAL: coult not open file: " << globalOpts.file << endl;

+   cerr << "FATAL: could not open file: " << globalOpts.file << endl;

    exit(1);

  }

--- libvcflib.orig/src/permuteGPATsmoother.cpp

+++ libvcflib/src/permuteGPATsmoother.cpp

@@ -170,7 +170,7 @@

    }

  }

  else{

-   cerr << "FATAL: coult not open file: " << globalOpts.file << endl;

+   cerr << "FATAL: could not open file: " << globalOpts.file << endl;

    exit(1);

  }

@@ -214,7 +214,7 @@

    }   

  }

  else{

-   cerr << "FATAL: coult not open file: " << globalOpts.file << endl;

+   cerr << "FATAL: could not open file: " << globalOpts.file << endl;

    exit(1);

  }

--- libvcflib.orig/src/permuteRegions.cpp

+++ libvcflib/src/permuteRegions.cpp

@@ -340,7 +340,7 @@

    }

  }

  else{

-   cerr << "FATAL: coult not open file: " << globalOpts.file << endl;

+   cerr << "FATAL: could not open file: " << globalOpts.file << endl;

    exit(1);

  }

--- libvcflib.orig/src/permuteSmooth.cpp

+++ libvcflib/src/permuteSmooth.cpp

@@ -356,7 +356,7 @@

    }

  }

  else{

-   cerr << "FATAL: coult not open file: " << globalOpts.file << endl;

+   cerr << "FATAL: could not open file: " << globalOpts.file << endl;

    exit(1);

  }

--- libvcflib.orig/src/plotHaps.cpp

+++ libvcflib/src/plotHaps.cpp

@@ -281,7 +281,7 @@

       }

     }

     else{

-      cerr << "FATAL: must specifiy a region" << endl;

+      cerr << "FATAL: must specify a region" << endl;

       printHelp();

       return 1;

     }