minor edit

hairs-src/extracthairs.c

@@ -33,7 +33,7 @@ int PARSEINDELS = 0;
 int SINGLEREADS = 0;
 int LONG_READS = 0;
 int REALIGN_VARIANTS = 0;
-int ESTIMATE_PARAMS = 1; // estimate realignment parameters from BAM 
+int ESTIMATE_PARAMS = 0; // estimate realignment parameters from BAM 
 //int QVoffset = 33; declared in samread.h
 FILE* logfile;
 int PFLAG = 1;
@@ -110,8 +110,8 @@ void print_options() {
     fprintf(stderr, "--ref <FILENAME> : reference sequence file (in fasta format, gzipped is okay), optional but required for indels, should be indexed\n");
     fprintf(stderr, "--out <FILENAME> : output filename for haplotype fragments, if not provided, fragments will be output to stdout\n");
     fprintf(stderr, "--region <chr:start-end> : chromosome and region in BAM file, useful to process individual chromosomes or genomic regions \n\n");
-    //fprintf(stderr, "--sumall <0/1> : set to 1 to use sum of all local alignments approach (only with long reads), default = 0 \n\n");
-    fprintf(stderr, "--ep <0/1> : set to 1 to estimate HMM parameters from aligned reads (only with long reads), default = 1 \n\n");
+    fprintf(stderr, "--ep <0/1> : set to 1 to estimate HMM parameters from aligned reads (only with long reads), default = 0\n\n");
+    //fprintf(stderr, "--sumall <0/1> : set to 1 to use sum of all local alignments approach (only with long reads), default = 1 \n\n");
 }
 
 void check_input_0_or_1(char* x){