Change default max depth for bedcov.#1970
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The -d option is used for specifying the minimum depth we need to meet in order to count bases covered with at least that depth in a new column. It also ups the bam_mplp_set_maxcnt mpileup limit from 64000 to the '-d' value if bigger. Therefore extremely deep data requires the use of '-d' to count bases even when it's not interested in the additional column. Changed the default to be INT_MAX (every read is counted) and added a new --max-depth option to control this so we can limit it for problematic files if desired. Also fixed usage statement formatting. Fixes samtools#1950
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The -d option is used for specifying the minimum depth we need to meet in order to count bases covered with at least that depth in a new column. It also ups the bam_mplp_set_maxcnt mpileup limit from 64000 to the '-d' value if bigger. Therefore extremely deep data requires the use of '-d' to count bases even when it's not interested in the additional column. Changed the default to be INT_MAX (every read is counted) and added a new --max-depth option to control this so we can limit it for problematic files if desired. Also fixed usage statement formatting. Fixes samtools#1950
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The -d option is used for specifying the minimum depth we need to meet in order to count bases covered with at least that depth in a new column. It also ups the bam_mplp_set_maxcnt mpileup limit from 64000 to the '-d' value if bigger.
Therefore extremely deep data requires the use of '-d' to count bases even when it's not interested in the additional column.
Changed the default to be INT_MAX (every read is counted) and added a new --max-depth option to control this so we can limit it for problematic files if desired. (It is unfortunate that in mpileup
-dis short for--max-depthand here it is a minimum depth instead.)Also fixed usage statement formatting.
Fixes #1950