From c14151c294b7e5984699822312edaf263eb95843 Mon Sep 17 00:00:00 2001 From: sooheelee Date: Tue, 10 Jan 2017 12:16:44 -0500 Subject: [PATCH 1/3] Update SAMRecord.java - Three variable descriptions changed: getAlignmentStart, setAlignmentStart and getAlignmentEnd. Before, each read, "position of the clipped sequence," and now each reads, "position of the sequence remaining after clipping," for all three variable descriptions. - In addition, took liberty to clarify "or 0 if there is no position" further. Now reads, "If no position, as would occur e.g. for the unmapped mate of a singly mapping pair, returns 0." --- src/main/java/htsjdk/samtools/SAMRecord.java | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/src/main/java/htsjdk/samtools/SAMRecord.java b/src/main/java/htsjdk/samtools/SAMRecord.java index 13ec3860a..2a5a4e1a1 100644 --- a/src/main/java/htsjdk/samtools/SAMRecord.java +++ b/src/main/java/htsjdk/samtools/SAMRecord.java @@ -572,14 +572,14 @@ protected static String resolveNameFromIndex(final int referenceIndex, final SAM } /** - * @return 1-based inclusive leftmost position of the clipped sequence, or 0 if there is no position. + * @return 1-based inclusive leftmost position of the sequence remaining after clipping. If no position, as would occur e.g. for the unmapped mate of a singly mapping pair, returns 0. */ public int getAlignmentStart() { return mAlignmentStart; } /** - * @param value 1-based inclusive leftmost position of the clipped sequence, or 0 if there is no position. + * @param value 1-based inclusive leftmost position of the sequence remaining after clipping. If no position, e.g. for unmapped mate of a singly mapping pair, returns 0. */ public void setAlignmentStart(final int value) { mAlignmentStart = value; @@ -590,7 +590,7 @@ public void setAlignmentStart(final int value) { } /** - * @return 1-based inclusive rightmost position of the clipped sequence, or 0 read if unmapped. + * @return 1-based inclusive rightmost position of the sequence remaining after clipping. If no position, e.g. for unmapped mate of a singly mapping pair, returns 0. */ public int getAlignmentEnd() { if (getReadUnmappedFlag()) { From 3c963d890128cb5e871001665898d8864e904760 Mon Sep 17 00:00:00 2001 From: sooheelee Date: Tue, 10 Jan 2017 12:19:24 -0500 Subject: [PATCH 2/3] Update SAMRecord.java --- src/main/java/htsjdk/samtools/SAMRecord.java | 9 ++++++--- 1 file changed, 6 insertions(+), 3 deletions(-) diff --git a/src/main/java/htsjdk/samtools/SAMRecord.java b/src/main/java/htsjdk/samtools/SAMRecord.java index 2a5a4e1a1..ed6f99d0e 100644 --- a/src/main/java/htsjdk/samtools/SAMRecord.java +++ b/src/main/java/htsjdk/samtools/SAMRecord.java @@ -572,14 +572,16 @@ protected static String resolveNameFromIndex(final int referenceIndex, final SAM } /** - * @return 1-based inclusive leftmost position of the sequence remaining after clipping. If no position, as would occur e.g. for the unmapped mate of a singly mapping pair, returns 0. + * @return 1-based inclusive leftmost position of the sequence remaining after clipping. + * If no position, as would occur e.g. for the unmapped mate of a singly mapping pair, returns 0. */ public int getAlignmentStart() { return mAlignmentStart; } /** - * @param value 1-based inclusive leftmost position of the sequence remaining after clipping. If no position, e.g. for unmapped mate of a singly mapping pair, returns 0. + * @param value 1-based inclusive leftmost position of the sequence remaining after clipping. + * If no position, e.g. for unmapped mate of a singly mapping pair, returns 0. */ public void setAlignmentStart(final int value) { mAlignmentStart = value; @@ -590,7 +592,8 @@ public void setAlignmentStart(final int value) { } /** - * @return 1-based inclusive rightmost position of the sequence remaining after clipping. If no position, e.g. for unmapped mate of a singly mapping pair, returns 0. + * @return 1-based inclusive rightmost position of the sequence remaining after clipping. + * If no position, e.g. for unmapped mate of a singly mapping pair, returns 0. */ public int getAlignmentEnd() { if (getReadUnmappedFlag()) { From 46dcdd1b841bcbd36a3092b02f7023ff45deb5fd Mon Sep 17 00:00:00 2001 From: sooheelee Date: Tue, 10 Jan 2017 17:01:15 -0500 Subject: [PATCH 3/3] Update SAMRecord.java based on feedback Now reads "1-based inclusive leftmost position of the sequence remaining after clipping, or 0 if there is no position, e.g. for unmapped read." --- src/main/java/htsjdk/samtools/SAMRecord.java | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/src/main/java/htsjdk/samtools/SAMRecord.java b/src/main/java/htsjdk/samtools/SAMRecord.java index ed6f99d0e..9f03b2312 100644 --- a/src/main/java/htsjdk/samtools/SAMRecord.java +++ b/src/main/java/htsjdk/samtools/SAMRecord.java @@ -572,16 +572,16 @@ protected static String resolveNameFromIndex(final int referenceIndex, final SAM } /** - * @return 1-based inclusive leftmost position of the sequence remaining after clipping. - * If no position, as would occur e.g. for the unmapped mate of a singly mapping pair, returns 0. + * @return 1-based inclusive leftmost position of the sequence remaining after clipping, or 0 + * if there is no position, e.g. for unmapped read. */ public int getAlignmentStart() { return mAlignmentStart; } /** - * @param value 1-based inclusive leftmost position of the sequence remaining after clipping. - * If no position, e.g. for unmapped mate of a singly mapping pair, returns 0. + * @param value 1-based inclusive leftmost position of the sequence remaining after clipping or 0 + * if there is no position, e.g. for unmapped read. */ public void setAlignmentStart(final int value) { mAlignmentStart = value; @@ -592,8 +592,8 @@ public void setAlignmentStart(final int value) { } /** - * @return 1-based inclusive rightmost position of the sequence remaining after clipping. - * If no position, e.g. for unmapped mate of a singly mapping pair, returns 0. + * @return 1-based inclusive rightmost position of the sequence remaining after clipping or 0 + * if there is no position, e.g. for unmapped read. */ public int getAlignmentEnd() { if (getReadUnmappedFlag()) {