Changes since v0.4.2:

• Removed the indexing step to save the pre-processing time and instead tasks are distributed while parsing the bam file
• The read modified bed file now contains the number of reads in the 4th column
• Added some tests for merging and sorting blocks
• Fixed memory leaks

Fixed a bug in the marker mode

• Fixed a bug in the tpool code
• Open input bed file in the read only mode since they it might be write-protected

• Added the multi-threading feature
• Added the program secphase_index for building a secphase-specific index file for a bam file sorted by read name
• Updated documentation

• Added parameter --inputVcf, -v for taking a phased vcf file to be used for phasing alignments to a diploid/dual assembly.
• Added parameter --variantBed, -B for subsetting variants that are going to be applied on the assembly and helping the phasing process.
• Added parameter --minVariantMargin, -g for receiving the minimum size of the window that has to created around each variant. The overlapping windows will be merged. If the size of an indel is greater than this value, the window will be twice as large as the indel length.
• Added parameter --minGQ, -G for filtering the phased variants with their genotype quality lower than this value.
• Added parameter --disableMarkerMode, -M.
• Added parameter --outDir, -o , --prefix, -P for creating output log and bed files in the given directory with the given prefix.
• Changed the default value for --primMarginRandom to 0. This means by default if a secondary alignment has the same score as the primary alignment Secphase will not modify it.
• If there are multiple secondary alignments with the maximum score (and all of them with score higher than the primary alignment), Secphase will select one of them randomly.
• Added the script find_homozygous_regions.py for finding homozygous regions in a phased diploid assembly.
• Added edlib as a submodule.
• Split the main code into multiple modules; ptBlock , ptAlignment , ptMarker and ptVariant.
• Updated htslib version to 1.17 in the docker image

• Added the new parameter --primMarginRandom.
• Fixed some minor bugs
• Output start/end positions in the output log file
• Added presets '--hifi' and '--ont'

The first release of Secphase