misha - 4.3.13

misha 4.3.13

• Added directional neighbor finding functions:
  • gintervals.neighbors.upstream() - Find upstream neighbors relative to query strand
  • gintervals.neighbors.downstream() - Find downstream neighbors relative to query strand
    
  • gintervals.neighbors.directional() - Find both upstream and downstream neighbors
• Added use_intervals1_strand parameter to gintervals.neighbors() to use query intervals' strand for distance directionality.
• Added warn.ignored.strand parameter to gintervals.neighbors() to control warnings when query strand is ignored.
• Fixed a bug in gintervals.neighbors: a stack imbalance in the C++ code in very rare cases of 2D intervals.
• Fixed errors in regression tests of gintervals.neighbors due to unbalanced rprotect calls.

misha 4.3.12

• Added gintervals.normalize and gintervals.annotate functions.
• Fixed errors in m1-asan build.

misha 4.3.11

• Removed C++14 requirement.

misha 4.3.9

• Fixed a bug in pwm and kmer virtual track functions: iterator shifts were not applied.
• Internal: address CRAN rchk notes and improve memory protection.

misha 4.3.8

• Added colnames parameter to gintervals.mapply function.
• Added attrs parameter to gtrack.import function.
• Added created.user default attribute in track creation functions.
• Support BED files in gtrack.import function.

misha 4.3.7

• Added gtrack.create_dense function - creates a dense track from an intervals and values.
• Fixed compilation error in old versions of macOS (clock_gettime is missing).
• Fixed a bug in gtrack.import_bigwig: intern argument was not passed to system calls.

- C++
Published by aviezerl 9 months ago

misha - misha 4.3.6

• Fixed memory alignment issues in clang-UBSAN.
  

- C++
Published by aviezerl about 1 year ago

misha - misha 4.3.5

• Bug fix in "coverage" virtual track function: incorrect results on some cases when query intervals where from different chromosomes.

- C++
Published by aviezerl over 1 year ago

misha - misha 4.3.4

• Added "kmer.count" and "kmer.frac" virtual track functions that calculate the number of k-mers and the fraction of k-mers in the current iterator interval.

- C++
Published by aviezerl over 1 year ago

misha - 4.3.3

misha 4.3.3

• Added "coverage" virtual track function that calculates the fraction that iterator intervals are covered by given source intervals.

misha 4.3.2

• Added requirement for C++14 standard.

- C++
Published by aviezerl over 1 year ago

misha - misha 4.3.1

• Fixed compilation issue on ubuntu devel.

- C++
Published by aviezerl over 1 year ago

misha - Misha 4.3.0

misha 4.3.0

• Added PWM functions: "pwm", "pwm.max" and "pwm.max.pos" are new virtual track functions.
• Added grevcomp function (reverse complement of a DNA sequence).

- C++
Published by aviezerl over 1 year ago

misha - Misha 4.2.13

misha 4.2.13

• Added gdb.create_genome function.
• removed non-API calls to R: R_curErrorBuf, SET_TYPEOF

misha 4.2.12

• Fixed noRemap additional issue by adding Rf_ prefix in the c++ code.
• Removed non-API calls to R in the C++ code.

misha 4.2.10

• Fixed a bug in gtrack.import from bigwig.

misha 4.2.9

• Fixed compilation issues in M1 Mac.

- C++
Published by aviezerl over 1 year ago

misha - misha 4.2.8

• Fixed "mat string is not a string literal" warnings.

- C++
Published by aviezerl over 2 years ago

misha - misha 4.2.6

• ALLGENOME is now only soft deprecated in order to support old misha scripts.
• Fixed compilation issues with gcc-UBSAN and LTO.

- C++
Published by aviezerl over 2 years ago

misha - misha 4.2.3

• Added gtrack.create_dirs function.
• Fixed a bug in gcluster.run.
• Updated documentation of gintervals.neighbors.

- C++
Published by aviezerl over 2 years ago