version 1.18.0

1.18.0 (2023-07-05)

• Add --include_allchr option to avoid an error if the chromosomes in the genome_table file do not begin with "chr" (see #8).

1.17.2 (2023-07-04)

• Add genometable files for various genome build in data/genometable

1.17.1 (2023-02-19)

• drompa+: Suppress the warning message "Warning: chrN has no gene." if the gene annotation file has no genes in the specified chromosome.

1.17.0 (2022-11-24)

• drompa+: Add --smoothingtype option to allow the average normalization, which is consistent with that of DROMPA3.

1.16.1 (2022-10-11)

• drompa+ PROFILE: change ymin value for --ptype 2 option

version 1.16.0

1.16.0 (2022-10-01)

• Bug fix in PROFILE --ptype 2 option (divide gene into 100 subregions): skip genes if the extended length exceeds the chromosome length
• Change the y-axis for --ptype 2 --stype 1 (ChIP/Input enrichment) from log scale to linear scale

1.15.4 (2022-09-28)

• Bug fix: remove ARS information from SGD features which are old.

1.15.3 (2022-08-25)

• Add "gpos33" and "gpos66" to the ideogram stain annotation.

1.15.2 (2022-08-05)

• Bug fix: remove "peak coverage" header from stats file when calculating FRiP score.
• Modify otherbins/parsestats4DROMPAplus.pl to output FRiP score always.

1.15.1 (2022-07-27)

• Add error messages when the format of supplied genometable/mptable files is wrong.
• Add error message when specified BED files are missing.

1.15.0 (2022-06-28)

• drompa+: Bug fix of not highlighting peak regions when specifying the peak list in -i option

1.14.1 (2022-05-10)

• parse2wig+: fixed the error when O. sativa genome is applied ("chrN" -> "ChrN")

version 1.14.0

1.14.0 (2022-04-20)

• parse2wig+: remove --allchr option. Now parse2wig+ always considers all chromosomes to estimate fragment length

version 1.13.0

1.13.0 (2022-04-10)

• parse2wig+: fixed the bug that the FRiP score always becomes zero

version 1.12.3

1.12.2 (2022-04-09)

• parse2wig+: bug fix in the error when the F3 length (read length) is too short (e.g., 1~3)

1.12.1 (2021-10-14)

• drompa+ PROFILE: bug fix for counting sites
• drompa+ PROFILE: include genes <1kbp long (before they were omitted)

1.12.0 (2021-10-13)

• drompa+ PROFILE: add --fixedlengthfromgene for --ptype 2 to use fixed length for outside of gene body

1.11.2 (2021-09-02)

parse2wig+: Bug fix to avoid overflow when a big constant value is supplied to --nrpm

1.11.1 (2021-08-29)

drompa+: Bug fix in getmax function ("Error: Invalid i for WigArray")

1.11.0 (2021-07-31)

• drompa+: Tuning the thining approach for read visualization (random -> max(abs(value)) for each windows)

1.10.1 (2021-07-08)

• drompa+: Modify the width for calculating p-inter (100kbp -> 1k bins)

version 1.10.0

• drompa+: Modify to allow bedGraph/bigWig files with variable step.
• drompa+: Bug fix when a single sample is specified multiple times with different binsize (5th string in -i)
• parse2wig+: Bug fix when parsing a SAM/BAM file mapped on a single fasta.
• Add "genometable.mm9.txt" in "data" folder.
• drompa+: Bug fix when the smoothing width is larger than the array size.
• drompa+: Add an error message when specifying a chromosome name by --chr that is not in the genometable file.
• drompa+: Bug fix for x memories when specifying a large value to --ls
• fixed typo
• drompa+: Bug fix that the y-axis of read distribution boxes becomes too bold when applying large binsize
• drompa+: Accept color information in BED12 file
• drompa+: Add --offbedname option to omit bed name
• drompa+: Allow BEDPE format for --inter option

version 1.8.6

• drompa+: Bug fix in reading bedGraph files generated by other tools
• drompa+: Change label (from full path to basename) when it is not explicitly specified
• drompa+: Add error message when supplying invalid bedGraph file
• Update email address
• drompa+: Modify parseGTF to allow gene id having transcript_id only
• drompa+: Add an error message when specifying an illegal BED file for -r option
• Bug fix: Gene annotation label for Ensembl data
• Remove printRefFlat function
• Bug fix: switch boost::bind to std::bind to avoid compilation error depend on the version of a compiler

version 1.8.1

• BED-formatted peak file is also generated in addition to TSV-formatted one

version 1.8.0

This repository was mistakenly deleted was remade with the latest version.

version 1.6.0

v1.6.0

Update README.md