Can we get the offset of the first alignment within a range?
The answer seems to be "no".
module HMM | |
using Distributions | |
import Distributions.rand | |
import Distributions.fit | |
immutable HiddenMarkovModel{TP, K} | |
theta::Vector{TP} | |
A::Matrix{Float64} |
#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() |
xcsdc |
Can we get the offset of the first alignment within a range?
The answer seems to be "no".
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:
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:
#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; |
module HMM | |
using Distributions | |
import Distributions.rand | |
import Distributions.fit | |
immutable HiddenMarkovModel{TP, K} | |
theta::Vector{TP} | |
A::Matrix{Float64} |
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