Merge pull request #34 from karel-brinda/devel

Ococo 0.1.2.7

Makefile

@@ -39,7 +39,7 @@ readme:
 	f=$$(mktemp);\
 	  echo $$f;\
 	  sed '/USAGE-BEGIN/q' README.md >> $$f; \
-	  printf -- '-->\n```' >> $$f; \
+	  printf -- '-->\n```\n' >> $$f; \
 	  man ./ococo.1 | col -b | grep -A999999 SYNO | grep -B99999999 AUTH | ghead -n -1 >> $$f; \
 	  printf '```\n<!---\n' >> $$f; \
 	  sed -n '/USAGE-END/,$$ p' README.md >> $$f;\

README.md

@@ -73,74 +73,74 @@ conda install -c bioconda ococo
 <!---
 USAGE-BEGIN
 -->
-
-```NAME
+```
 SYNOPSIS
        ococo -i <SAM/BAM file> [other options]
 
 DESCRIPTION
-       Ococo  is a program to call genomic consensus directly from an unsorted
-       SAM/BAM stream.
+       Ococo  is  a  program to call variants and a genomic consensus directly
+       from an unsorted SAM/BAM stream.
 
    Input options:
        -i, --input FILE
-              Input SAM/BAM file (- for standard input).
+	      Input SAM/BAM file (- for standard input).
 
        -f, --fasta-ref FILE
-              Initial FASTA reference (otherwise seq of N's is used).
+	      Initial FASTA reference (otherwise a seq of N's is used).
 
        -s, --stats-in FILE
-              Input statistics.
+	      Input statistics.
 
    Output options:
-       -F, --fasta-cons FILE FASTA file with consensus
+       -F, --fasta-cons FILE Print consensus in FASTA.
 
        -S, --stats-out FILE
-              Output statistics.
+	      Export statistics to a file.
 
        -V, --vcf-cons FILE
-              VCF file with updates of consensus (- for standard output)
+	      Print inferred variants in VCF (- for standard output).
 
        -P, --pileup FILE
-              Truncated pileup (- for standard output).
+	      Print SAMtools pileup (- for standard output).
 
        --verbose
-              Verbose mode (report every update of a counter).
+	      Use the verbose mode (report every update of a counter).
 
    Parameters for consensus calling:
        -x, --counters STR
-              Counter configuration [ococo16].
+	      Counter configuration [ococo32].
 
 
-              configuration   bits/counter   bits/position
-              ococo16         3              16
-              ococo32         7              32
-              ococo64         15             64
+	      configuration   bits/counter   bits/position
+	      ococo16	      3 	     16
+	      ococo32	      7 	     32
+	      ococo64	      15	     64
 
 
        -m, --mode STR
-              Mode [batch].
+	      Mode [batch].
 
 
-              mode        description
-              real-time   updates reported immediately
-              batch       updates reported after end of algn stream
+	      mode	  description
+	      real-time   updates reported immediately
+	      batch	  updates reported after end of algn stream
 
 
        -q, --min-MQ INT
-              Skip alignments with mapping quality smaller than INT [1].
+	      Skip alignments with mapping quality smaller than INT [1].
 
        -Q, --min-BQ INT
-              Skip bases with base quality smaller than INT [13].
+	      Skip bases with base quality smaller than INT [13].
 
        -w, --ref-weight INT
-              Initial counter value for nucleotides from ref [0].
+	      Initial counter value for nucleotides from ref [0].
 
        -c, --min-cov INT
-              Minimum coverage required for update [2].
+	      Minimum coverage required for update [2].
 
        -M, --maj-thres FLOAT
-              Majority threshold [0.51].
+	      Majority threshold [0.51].
+
 ```
 <!---
 USAGE-END

ococo.1

@@ -5,37 +5,38 @@ ococo \- Online variant and consensus caller
 .SH SYNOPSIS
 ococo -i <SAM/BAM file> [other options]
 .SH DESCRIPTION
-Ococo is a program to call genomic consensus directly from an unsorted
-SAM/BAM stream.
+Ococo is a program to call variants and a genomic consensus directly from an
+unsorted SAM/BAM stream.
 .SS "Input options:"
 .TP
 \fB\-i\fR, \fB\-\-input\fR FILE
 Input SAM/BAM file (\- for standard input).
 .TP
 \fB\-f\fR, \fB\-\-fasta\-ref\fR FILE
-Initial FASTA reference (otherwise seq of N's is used).
+Initial FASTA reference (otherwise a seq of N's is used).
 .TP
 \fB\-s\fR, \fB\-\-stats\-in\fR FILE
 Input statistics.
 .SS "Output options:"
 .HP
-\fB\-F\fR, \fB\-\-fasta\-cons\fR FILE FASTA file with consensus
+\fB\-F\fR, \fB\-\-fasta\-cons\fR FILE
+Print consensus in FASTA.
 .TP
 \fB\-S\fR, \fB\-\-stats\-out\fR FILE
-Output statistics.
+Export statistics to a file.
 .TP
 \fB\-V\fR, \fB\-\-vcf\-cons\fR FILE
-VCF file with updates of consensus (\- for standard output)
+Print inferred variants in VCF (\- for standard output).
 .TP
 \fB\-P\fR, \fB\-\-pileup\fR FILE
-Truncated pileup (\- for standard output).
+Print SAMtools pileup (\- for standard output).
 .TP
 \fB\-\-verbose\fR
-Verbose mode (report every update of a counter).
+Use the verbose mode (report every update of a counter).
 .SS "Parameters for consensus calling:"
 .TP
 \fB\-x\fR, \fB\-\-counters\fR STR
-Counter configuration [ococo16].
+Counter configuration [ococo32].
 
 .TS
 l	l	l	.
@@ -74,7 +75,7 @@ Minimum coverage required for update [2].
 \fB\-M\fR, \fB\-\-maj\-thres\fR FLOAT
 Majority threshold [0.51].
 .SH AUTHOR
-Written by Karel Brinda (kbrinda@hsph.harvard.edu).
+Karel Brinda (kbrinda@hsph.harvard.edu).
 .SH REPORTING BUGS
 Report bugs on https://github.com/karel-brinda/ococo/issues
 .SH EXAMPLES

src/params.cpp

@@ -9,8 +9,8 @@
 
 void ococo::params_t::init_default_values() {
     verbose               = false;
-    counters_str          = "ococo16";
-    counter_configuration = OCOCO16;
+    counters_str          = "ococo32";
+    counter_configuration = OCOCO32;
     mode                  = BATCH;
     mode_str              = "batch";
     strategy              = MAJORITY;

src/version.h

@@ -1,5 +1,5 @@
 #pragma once
 
 namespace ococo {
-static const char *OCOCO_VERSION = "0.1.2.6";
+static const char *OCOCO_VERSION = "0.1.2.7";
 }