dalexander

byStrand,noPolish settings incorrectly recognized as true by ccs under clang

Running ccs on my Mac (clang++), I get this failure:

[~/Dropbox/Sources/git-pbi/pbccs]$ bin/ccs --logLevel=DEBUG \
  --minZScore -100 --maxDropFrac 0.8 tests/data/100zmws.bam test.fq
Usage: ccs [OPTIONS] INPUT OUTPUT

ccs: error: option --byStrand: incompatible with --noPolish

dalexander

module HMM

using Distributions

import Distributions.rand
import Distributions.fit

immutable HiddenMarkovModel{TP, K}
    theta::Vector{TP}
    A::Matrix{Float64}

dalexander

#include "ReadName.hpp"

#include <exception>
#include <string>
#include <boost/xpressive/xpressive.hpp>
#include <boost/lexical_cast.hpp>

using std::string;
using boost::xpressive::smatch;
using boost::lexical_cast;

dalexander

Can we get the offset of the first alignment within a range?

The answer seems to be “no”. Building the iterator (sam_itr_queryi) does not seek, and the first time you use advance the iterator (bam_itr_next), you are already past the first read.

Here are the offsets of the first reads in the file, along with their [tStart, tEnd) spans:

dalexander

Can we get the offset of the first alignment within a range?

The answer seems to be “no”. Building the iterator (sam_itr_queryi) does not seek, and the first time you use advance the iterator (bam_itr_next), you are already past the first read.

Here are the offsets of the first reads in the file, along with their [tStart, tEnd) spans:

dalexander

Can we get the offset of the first alignment within a range?

The answer seems to be "no".

dalexander

xcsdc

dalexander

#light
#r "PacBio.Native.BamTools.dll"

open System
open PacBio.Native.BamTools


let reader = new BamReader()
reader.Open("/Users/dalexander/Data/082796.bam")
reader.LocateIndex()

dalexander

module HMM

using Distributions

import Distributions.rand
import Distributions.fit

immutable HiddenMarkovModel{TP, K}
    theta::Vector{TP}
    A::Matrix{Float64}

dalexander

#
# Push gaps forward in homopolymers
#
# Rewrite rule 1: XX    ===>  XX
#                 X-          -X
#
# Rewrite rule 2: X-    ===>  -X
#                 XX          XX
#
# Iterate until convergence.